Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbs Working: n-1-18.cluster.ucsf.bkslab.org:/scratch/xiaobo/194367/xbs-8058088.45 Result: /scratch/xiaobo/194367/xbs-8058088.45 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs 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/xbs mkdir: created directory `/scratch/xiaobo/194367' mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45' /scratch/xiaobo/194367/xbs-8058088.45 /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/194367/xbs-8058088.45/working' mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/protonate' Storing results in /scratch/xiaobo/194367/xbs-8058088.45/finished Working in /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 /scratch/xiaobo/194367/xbs-8058088.45/working/protonate /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Using inputs as protomers/tautomers. No processing done 456 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/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Bulk generating 3D conformations all protomers in /scratch/xiaobo/194367/xbs-8058088.45/working/3D mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/194367/xbs-8058088.45/working/protonate/xbs-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 ZINC001566302791 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building' mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001566302791 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/1 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001566302791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566302791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001566302791 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 10, 10, 10, 10, 3, 3, 5, 5, 5, 5, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3] 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001566302791 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/finished' Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791/0.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566302791 Building ZINC001566469527 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566469527 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/2 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1) `ZINC001566469527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566469527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001566469527 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 21, 21, 11, 21, 21, 21, 11, 2, 2, 2, 2, 5, 5, 2, 3, 11, 21, 21, 15, 21, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/3 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1) `ZINC001566469527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566469527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001566469527 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 21, 21, 11, 21, 21, 21, 11, 2, 2, 2, 2, 5, 5, 2, 3, 11, 21, 21, 20, 21, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001566469527 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 Building ZINC001566469527 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566469527 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 2) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1) `ZINC001566469527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566469527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001566469527 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 21, 21, 11, 21, 21, 21, 11, 2, 2, 2, 2, 5, 5, 2, 3, 11, 21, 21, 15, 21, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 3) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1) `ZINC001566469527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566469527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001566469527 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 21, 21, 11, 21, 21, 21, 11, 2, 2, 2, 2, 5, 5, 2, 3, 11, 21, 21, 20, 21, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001566469527 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566469527 Building ZINC001566658738 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566658738 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/4 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001566658738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566658738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001566658738 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 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, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 14, 14, 14, 14, 4, 4, 4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 42, 39, 13, 14, 15, 40, 41, 36] set([0, 1, 3, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/5 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001566658738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566658738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001566658738 none CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 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, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 15, 15, 15, 15, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001566658738 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 Building ZINC001566658738 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566658738 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 4) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001566658738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566658738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001566658738 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 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, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 14, 14, 14, 14, 4, 4, 4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 42, 39, 13, 14, 15, 40, 41, 36] set([0, 1, 3, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 5) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001566658738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566658738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001566658738 none CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 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, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 15, 15, 15, 15, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001566658738 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001566658738 Building ZINC001568616527 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568616527 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/6 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568616527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616527 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 27, 27, 27, 27, 27, 27, 48, 48, 48, 49, 49, 49, 49, 49, 49, 27, 4, 4, 4, 4, 4, 4, 3, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 27] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/7 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568616527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616527 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 24, 24, 24, 24, 24, 24, 46, 46, 46, 47, 47, 47, 47, 47, 47, 24, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 24, 24, 47, 47, 47, 47, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001568616527 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 Building ZINC001568616527 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568616527 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 6) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568616527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616527 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 27, 27, 27, 27, 27, 27, 48, 48, 48, 49, 49, 49, 49, 49, 49, 27, 4, 4, 4, 4, 4, 4, 3, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 27] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 7) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568616527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616527 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 24, 24, 24, 24, 24, 24, 46, 46, 46, 47, 47, 47, 47, 47, 47, 24, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 24, 24, 47, 47, 47, 47, 24, 24] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001568616527 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616527 Building ZINC001568616528 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568616528 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/8 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568616528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616528 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 25, 25, 25, 25, 25, 25, 45, 45, 45, 48, 48, 45, 47, 48, 48, 25, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25, 48, 48, 48, 48, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/9 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568616528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616528 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 27, 27, 27, 27, 27, 27, 48, 48, 48, 50, 50, 49, 49, 50, 50, 27, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001568616528 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 Building ZINC001568616528 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568616528 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 8) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568616528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616528 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 25, 25, 25, 25, 25, 25, 45, 45, 45, 48, 48, 45, 47, 48, 48, 25, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25, 48, 48, 48, 48, 25, 25] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 9) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)C1) `ZINC001568616528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568616528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568616528 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(=O)(=O)c2ccc(Br)cc2)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.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 27, 27, 27, 27, 27, 27, 48, 48, 48, 50, 50, 49, 49, 50, 50, 27, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001568616528 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568616528 Building ZINC001568670661 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568670661 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/10 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1) `ZINC001568670661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568670661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001568670661 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 5, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 33, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/11 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1) `ZINC001568670661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568670661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001568670661 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 13, 13, 4, 10, 10, 10, 10, 30, 10, 10, 10, 10, 10, 10, 10, 10] 150 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]) total number of confs: 94 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001568670661 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 Building ZINC001568670661 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568670661 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 10) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1) `ZINC001568670661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568670661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001568670661 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 5, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 33, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 11) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1) `ZINC001568670661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568670661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001568670661 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(O)(c2ccccc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 13, 13, 4, 10, 10, 10, 10, 30, 10, 10, 10, 10, 10, 10, 10, 10] 150 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]) total number of confs: 94 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001568670661 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001568670661 Building ZINC001569535603 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535603 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/12 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/12' -> `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(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535603 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 3, 3, 13, 13, 3, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/13 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/13' -> `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(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535603 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 6, 6, 2, 2, 2, 2, 2, 2, 14, 14, 2, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535603 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 Building ZINC001569535603 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535603 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 12) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535603 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 3, 3, 13, 13, 3, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 13) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535603 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 6, 6, 2, 2, 2, 2, 2, 2, 14, 14, 2, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535603 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535603 Building ZINC001569535604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/14 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/14' -> `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(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535604 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 18, 18, 7, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 4, 4, 1, 1, 1, 1, 7, 7, 18, 18, 7, 18] 50 rigid atoms, others: [43, 5, 38, 7, 8, 9, 10, 11, 12, 44, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/15 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/15' -> `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(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535604 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 17, 17, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 1, 4, 4, 1, 1, 1, 1, 7, 7, 17, 17, 7, 17] 50 rigid atoms, others: [43, 5, 38, 7, 8, 9, 10, 11, 12, 44, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 Building ZINC001569535604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 14) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535604 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 18, 18, 7, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 4, 4, 1, 1, 1, 1, 7, 7, 18, 18, 7, 18] 50 rigid atoms, others: [43, 5, 38, 7, 8, 9, 10, 11, 12, 44, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 15) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535604 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 17, 17, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 1, 4, 4, 1, 1, 1, 1, 7, 7, 17, 17, 7, 17] 50 rigid atoms, others: [43, 5, 38, 7, 8, 9, 10, 11, 12, 44, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535604 Building ZINC001569535605 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535605 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/16 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/16' -> `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(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535605 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 6, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 1, 4, 4, 1, 1, 1, 1, 6, 6, 16, 16, 6, 16] 50 rigid atoms, others: [43, 38, 7, 8, 9, 10, 11, 12, 44, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 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/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/17 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/17' -> `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(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535605 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2, 4, 4, 16, 16, 4, 16] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535605 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 Building ZINC001569535605 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535605 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 16) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535605 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 6, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 1, 4, 4, 1, 1, 1, 1, 6, 6, 16, 16, 6, 16] 50 rigid atoms, others: [43, 38, 7, 8, 9, 10, 11, 12, 44, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 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/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 17) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535605 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 4, 4, 4, 16, 16, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 2, 5, 5, 2, 2, 2, 2, 4, 4, 16, 16, 4, 16] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535605 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535605 Building ZINC001569535606 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535606 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/18 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/18' -> `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(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535606 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 3, 3, 15, 15, 3, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/19 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/19' -> `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(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535606 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 3, 3, 13, 13, 3, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535606 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 Building ZINC001569535606 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569535606 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 18) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569535606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535606 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 3, 3, 15, 15, 3, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 19) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001569535606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569535606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001569535606 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 3, 3, 13, 13, 3, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001569535606 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001569535606 Building ZINC001570023531 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001570023531 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/20 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1) `ZINC001570023531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570023531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001570023531 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 8, 15, 29, 29, 30, 36, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 15, 15, 36, 36, 37, 37, 37, 37, 37, 15, 15] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/21 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1) `ZINC001570023531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570023531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001570023531 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 9, 14, 29, 29, 30, 36, 37, 37, 37, 37, 37, 14, 14, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 14, 14, 36, 36, 37, 37, 37, 37, 37, 14, 14] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570023531 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 Building ZINC001570023531 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001570023531 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 20) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1) `ZINC001570023531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570023531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001570023531 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 15, 15, 8, 15, 29, 29, 30, 36, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 15, 15, 36, 36, 37, 37, 37, 37, 37, 15, 15] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 21) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1) `ZINC001570023531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570023531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001570023531 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)OCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 9, 14, 29, 29, 30, 36, 37, 37, 37, 37, 37, 14, 14, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 14, 14, 36, 36, 37, 37, 37, 37, 37, 14, 14] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001570023531 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570023531 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570023531 Building ZINC001570304187 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001570304187 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/22 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/23 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/24 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/24' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/25 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/25' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570304187 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 Building ZINC001570304187 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001570304187 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 22) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 23) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 24) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 25) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570304187 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 Building ZINC001570304187 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001570304187 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 22) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 23) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 24) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 25) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570304187 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 Building ZINC001570304187 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001570304187 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 22) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 23) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 24) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 6, 18, 18, 18, 18, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 4, 4, 1, 2, 18, 18, 26, 26, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 25) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1) `ZINC001570304187.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001570304187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001570304187 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(CC(F)(F)F)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 28, 28, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 19, 19, 28, 28, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570304187 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570304187 Building ZINC001570542543 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001570542543 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/26 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001570542543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570542543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001570542543 none O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 16, 13, 16, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/27 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001570542543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570542543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001570542543 none O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 17, 17, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570542543 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 Building ZINC001570542543 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001570542543 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 26) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001570542543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570542543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001570542543 none O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 16, 13, 16, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 27) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001570542543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570542543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001570542543 none O=C(NCc1ccc(CN2CCS(=O)(=O)CC2)cc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 5, 5, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 17, 17, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001570542543 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001570542543 Building ZINC001583150769 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583150769 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/28 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1) `ZINC001583150769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583150769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001583150769 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'O.3', 'C.3', 'F', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 12, 18, 18, 18, 18, 18, 42, 42, 42, 42, 18, 12, 12, 12, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/29 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1) `ZINC001583150769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583150769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001583150769 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'O.3', 'C.3', 'F', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 17, 17, 17, 17, 17, 40, 40, 40, 40, 17, 11, 11, 11, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583150769 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 Building ZINC001583150769 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583150769 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 28) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1) `ZINC001583150769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583150769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001583150769 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'O.3', 'C.3', 'F', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 12, 18, 18, 18, 18, 18, 42, 42, 42, 42, 18, 12, 12, 12, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 29) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1) `ZINC001583150769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583150769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001583150769 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(OC(F)(F)F)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'O.3', 'C.3', 'F', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 17, 17, 17, 17, 17, 40, 40, 40, 40, 17, 11, 11, 11, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583150769 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583150769 Building ZINC001583154190 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583154190 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/30 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1) `ZINC001583154190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583154190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154190 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 16, 4, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 16, 16, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/31 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1) `ZINC001583154190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583154190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154190 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 3, 3, 3, 3, 11, 11, 3, 10, 10, 10, 10, 11, 11, 11, 11, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583154190 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 Building ZINC001583154190 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583154190 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 30) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1) `ZINC001583154190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583154190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154190 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 16, 4, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 16, 16, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 31) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1) `ZINC001583154190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583154190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154190 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 3, 3, 3, 3, 11, 11, 3, 10, 10, 10, 10, 11, 11, 11, 11, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583154190 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154190 Building ZINC001583154192 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583154192 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/32 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1) `ZINC001583154192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583154192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154192 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 11, 11, 11, 11, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/33 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1) `ZINC001583154192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583154192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154192 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 16, 4, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 10, 10, 9, 10, 10, 10, 9, 4, 4, 4, 4, 16, 16, 4, 9, 9, 9, 9, 10, 10, 10, 10, 9, 9] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583154192 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 Building ZINC001583154192 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583154192 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 32) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1) `ZINC001583154192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583154192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154192 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 3, 3, 3, 3, 9, 9, 3, 10, 10, 10, 10, 11, 11, 11, 11, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 33) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1) `ZINC001583154192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583154192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001583154192 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 16, 4, 1, 1, 1, 2, 5, 5, 9, 9, 9, 9, 9, 9, 10, 10, 9, 10, 10, 10, 9, 4, 4, 4, 4, 16, 16, 4, 9, 9, 9, 9, 10, 10, 10, 10, 9, 9] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583154192 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583154192 Building ZINC001583528611 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583528611 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/34 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583528611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528611 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 8, 8, 5, 8, 8, 4, 4, 4, 4, 12, 12, 4, 3, 15, 15, 15, 15, 15, 15, 15, 8, 8, 5, 8, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/35 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583528611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528611 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 10, 10, 7, 10, 10, 4, 4, 4, 4, 11, 11, 4, 4, 17, 17, 17, 17, 17, 17, 17, 10, 10, 7, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583528611 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 Building ZINC001583528611 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583528611 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 34) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583528611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528611 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 8, 8, 5, 8, 8, 4, 4, 4, 4, 12, 12, 4, 3, 15, 15, 15, 15, 15, 15, 15, 8, 8, 5, 8, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 35) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583528611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528611 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 10, 10, 7, 10, 10, 4, 4, 4, 4, 11, 11, 4, 4, 17, 17, 17, 17, 17, 17, 17, 10, 10, 7, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583528611 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528611 Building ZINC001583528614 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583528614 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/36 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583528614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528614 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 10, 10, 7, 10, 10, 4, 4, 4, 4, 11, 11, 4, 4, 18, 18, 18, 18, 18, 18, 18, 10, 10, 7, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/37 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583528614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528614 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 9, 9, 5, 9, 9, 4, 4, 4, 4, 12, 12, 4, 3, 16, 16, 16, 16, 16, 16, 16, 9, 9, 5, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583528614 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 Building ZINC001583528614 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583528614 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 36) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583528614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528614 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 10, 10, 7, 10, 10, 4, 4, 4, 4, 11, 11, 4, 4, 18, 18, 18, 18, 18, 18, 18, 10, 10, 7, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 37) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1) `ZINC001583528614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583528614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001583528614 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nc2ccccc2n1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 9, 9, 5, 9, 9, 4, 4, 4, 4, 12, 12, 4, 3, 16, 16, 16, 16, 16, 16, 16, 9, 9, 5, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001583528614 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001583528614 Building ZINC001584028714 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584028714 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/38 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1) `ZINC001584028714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584028714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028714 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 13, 13, 9, 13, 13, 13, 6, 3, 3, 3, 3, 9, 9, 3, 6, 6, 6, 6, 13, 13, 10, 13, 6, 6] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/39 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1) `ZINC001584028714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584028714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028714 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 15, 15, 11, 15, 15, 15, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 15, 15, 13, 15, 9, 9] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001584028714 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 Building ZINC001584028714 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584028714 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 38) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1) `ZINC001584028714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584028714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028714 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 13, 13, 9, 13, 13, 13, 6, 3, 3, 3, 3, 9, 9, 3, 6, 6, 6, 6, 13, 13, 10, 13, 6, 6] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 39) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1) `ZINC001584028714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584028714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028714 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 15, 15, 11, 15, 15, 15, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 15, 15, 13, 15, 9, 9] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001584028714 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028714 Building ZINC001584028715 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584028715 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/40 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1) `ZINC001584028715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584028715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028715 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 15, 15, 9, 15, 15, 15, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 15, 15, 13, 15, 9, 9] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/41 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1) `ZINC001584028715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584028715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028715 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 13, 13, 12, 13, 13, 13, 7, 2, 2, 2, 2, 8, 8, 2, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001584028715 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 Building ZINC001584028715 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584028715 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 40) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1) `ZINC001584028715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584028715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028715 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 15, 15, 9, 15, 15, 15, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 15, 15, 13, 15, 9, 9] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 41) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1) `ZINC001584028715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584028715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001584028715 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2ccccc2Br)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 13, 13, 12, 13, 13, 13, 7, 2, 2, 2, 2, 8, 8, 2, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001584028715 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584028715 Building ZINC001584729990 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584729990 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/42 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1) `ZINC001584729990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584729990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001584729990 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 29, 29, 29, 37, 41, 41, 37, 41, 41, 16, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 18, 18, 18, 37, 37, 41, 41, 37, 41, 41, 18] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/43 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1) `ZINC001584729990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584729990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001584729990 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 8, 17, 17, 17, 17, 17, 29, 29, 29, 38, 42, 42, 38, 42, 42, 17, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 17, 17, 17, 38, 38, 42, 42, 38, 42, 42, 17] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001584729990 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 Building ZINC001584729990 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584729990 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 42) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1) `ZINC001584729990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584729990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001584729990 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 29, 29, 29, 37, 41, 41, 37, 41, 41, 16, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 18, 18, 18, 37, 37, 41, 41, 37, 41, 41, 18] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 43) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1) `ZINC001584729990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584729990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001584729990 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 8, 17, 17, 17, 17, 17, 29, 29, 29, 38, 42, 42, 38, 42, 42, 17, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 17, 17, 17, 38, 38, 42, 42, 38, 42, 42, 17] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001584729990 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001584729990 Building ZINC001585245889 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585245889 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/44 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001585245889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585245889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001585245889 none O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 7, 10, 24, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 10, 10, 24, 42, 42, 42, 42, 42, 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, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/45 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001585245889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585245889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001585245889 none O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 4, 8, 28, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 28, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585245889 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 Building ZINC001585245889 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585245889 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 44) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001585245889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585245889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001585245889 none O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 7, 10, 24, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 10, 10, 24, 42, 42, 42, 42, 42, 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, 52, 53, 54]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 45) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001585245889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585245889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001585245889 none O=C(N1CCN(CCNS(=O)(=O)c2ccccc2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 4, 8, 28, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 28, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 20, 21, 22] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585245889 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585245889 Building ZINC001585275616 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585275616 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/46 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1) `ZINC001585275616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585275616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585275616 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 12, 21, 21, 24, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 1, 3, 3, 1, 2, 12, 12, 21, 21, 12, 24, 24, 37, 37, 37, 37, 37, 21] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/47 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1) `ZINC001585275616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585275616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585275616 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 12, 21, 21, 24, 36, 36, 36, 36, 36, 36, 36, 36, 20, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 21, 21, 12, 24, 24, 36, 36, 36, 36, 36, 21] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585275616 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 Building ZINC001585275616 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585275616 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 46) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1) `ZINC001585275616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585275616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585275616 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 12, 21, 21, 24, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 1, 3, 3, 1, 2, 12, 12, 21, 21, 12, 24, 24, 37, 37, 37, 37, 37, 21] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 47) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1) `ZINC001585275616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585275616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585275616 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cccc(Cn2cnc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 12, 21, 21, 24, 36, 36, 36, 36, 36, 36, 36, 36, 20, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 21, 21, 12, 24, 24, 36, 36, 36, 36, 36, 21] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585275616 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585275616 Building ZINC001585786638 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585786638 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/48 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585786638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585786638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585786638 none O=C(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 27, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 27, 34, 34, 34, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/49 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585786638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585786638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585786638 none O=C(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 27, 33, 33, 33, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 27, 36, 36, 36, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585786638 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 Building ZINC001585786638 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585786638 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 48) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585786638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585786638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585786638 none O=C(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 27, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 27, 34, 34, 34, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 49) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585786638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585786638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585786638 none O=C(NCCNS(=O)(=O)c1ccc(Cl)cc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 27, 33, 33, 33, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 27, 36, 36, 36, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585786638 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585786638 Building ZINC001585932140 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932140 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/50 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932140 none CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 9, 9, 9, 7, 7, 7, 7, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/51 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932140 none CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 4, 13, 13, 13, 13, 13, 13, 2, 2, 11, 11, 11, 10, 10, 10, 10, 2, 2, 2, 2, 13, 13, 4, 13, 2, 2, 2] 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: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932140 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 Building ZINC001585932140 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932140 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 50) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932140 none CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 9, 9, 9, 7, 7, 7, 7, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 51) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932140 none CO[C@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 4, 13, 13, 13, 13, 13, 13, 2, 2, 11, 11, 11, 10, 10, 10, 10, 2, 2, 2, 2, 13, 13, 4, 13, 2, 2, 2] 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: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932140 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932140 Building ZINC001585932141 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932141 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/52 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932141 none CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 8, 16, 16, 16, 16, 16, 16, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 16, 16, 16, 16, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/53 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932141 none CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 10, 10, 10, 7, 7, 7, 7, 2, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932141 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 Building ZINC001585932141 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932141 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 52) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932141 none CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 8, 16, 16, 16, 16, 16, 16, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 16, 16, 16, 16, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 53) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932141 none CO[C@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 10, 10, 10, 7, 7, 7, 7, 2, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932141 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932141 Building ZINC001585932142 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932142 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/54 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932142 none CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 9, 9, 9, 6, 6, 6, 6, 2, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/55 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932142 none CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 11, 11, 11, 7, 7, 7, 7, 2, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932142 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 Building ZINC001585932142 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932142 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 54) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932142 none CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 9, 9, 9, 6, 6, 6, 6, 2, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 55) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932142 none CO[C@@H]1CS(=O)(=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 11, 11, 11, 7, 7, 7, 7, 2, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932142 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932142 Building ZINC001585932143 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932143 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/56 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932143 none CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 3, 3, 10, 10, 10, 8, 8, 8, 8, 2, 3, 3, 3, 16, 16, 8, 16, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/57 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932143 none CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 10, 20, 20, 20, 20, 20, 20, 4, 4, 9, 9, 9, 8, 8, 8, 8, 2, 4, 4, 4, 20, 20, 12, 20, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932143 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 Building ZINC001585932143 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585932143 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 56) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585932143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932143 none CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 3, 3, 10, 10, 10, 8, 8, 8, 8, 2, 3, 3, 3, 16, 16, 8, 16, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 57) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001585932143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585932143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585932143 none CO[C@@H]1CS(=O)(=O)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 5, 7, 5, 14, 11, 11, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 10, 20, 20, 20, 20, 20, 20, 4, 4, 9, 9, 9, 8, 8, 8, 8, 2, 4, 4, 4, 20, 20, 12, 20, 4, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585932143 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585932143 Building ZINC001585991301 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585991301 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/58 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001585991301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585991301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585991301 none NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 19, 33, 33, 19, 19, 13, 19, 19, 13, 13, 13, 13, 6, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 33, 33, 19, 13, 19, 19, 13, 13, 13, 13, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/59 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001585991301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585991301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585991301 none NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 18, 31, 31, 18, 18, 12, 18, 18, 12, 12, 12, 12, 6, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 31, 31, 18, 12, 18, 18, 12, 12, 12, 12, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585991301 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 Building ZINC001585991301 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585991301 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 58) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001585991301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585991301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585991301 none NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 19, 33, 33, 19, 19, 13, 19, 19, 13, 13, 13, 13, 6, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 33, 33, 19, 13, 19, 19, 13, 13, 13, 13, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 59) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001585991301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585991301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585991301 none NS(=O)(=O)c1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 18, 31, 31, 18, 18, 12, 18, 18, 12, 12, 12, 12, 6, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 31, 31, 18, 12, 18, 18, 12, 12, 12, 12, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001585991301 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001585991301 Building ZINC001586015124 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586015124 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/60 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1) `ZINC001586015124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586015124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586015124 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 6, 10, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 10, 10, 3, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/61 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1) `ZINC001586015124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586015124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586015124 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 1, 5, 9, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 7, 7, 2, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586015124 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 Building ZINC001586015124 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586015124 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 60) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1) `ZINC001586015124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586015124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586015124 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 6, 10, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 10, 10, 3, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 61) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1) `ZINC001586015124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586015124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586015124 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cnn(c3ccccc3)c2CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 1, 5, 9, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 7, 7, 2, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586015124 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586015124 Building ZINC001586616495 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586616495 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/62 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001586616495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586616495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586616495 none CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 14, 15, 15, 15, 15, 15, 15, 14, 14, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 3, 3, 8, 8, 15, 15, 15, 15, 14, 14, 14, 14, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/63 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001586616495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586616495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586616495 none CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 40, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586616495 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 Building ZINC001586616495 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586616495 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 62) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001586616495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586616495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586616495 none CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 14, 15, 15, 15, 15, 15, 15, 14, 14, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 3, 3, 8, 8, 15, 15, 15, 15, 14, 14, 14, 14, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 63) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001586616495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586616495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586616495 none CN(CC1(c2ccc(Br)cc2)CC1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 40, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586616495 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586616495 Building ZINC001586715278 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586715278 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/64 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001586715278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586715278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001586715278 none COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 10, 15, 1, 10, 10, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 33, 33, 31, 30, 21, 21, 15, 15, 15, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/65 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001586715278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586715278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001586715278 none COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 10, 15, 1, 10, 10, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 33, 33, 30, 30, 21, 21, 15, 15, 15, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586715278 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 Building ZINC001586715278 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586715278 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 64) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001586715278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586715278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001586715278 none COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 10, 15, 1, 10, 10, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 33, 33, 31, 30, 21, 21, 15, 15, 15, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 65) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001586715278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586715278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001586715278 none COCCN(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 10, 15, 1, 10, 10, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 33, 33, 33, 30, 30, 21, 21, 15, 15, 15, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586715278 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586715278 Building ZINC001586913498 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586913498 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/66 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001586913498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586913498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586913498 none O=C(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 6, 14, 14, 14, 14, 26, 26, 26, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 14, 14, 14, 14, 1, 1, 2, 1, 1] 100 rigid atoms, others: [1, 36, 37, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/67 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001586913498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586913498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586913498 none O=C(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 7, 13, 13, 13, 13, 25, 25, 25, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 13, 13, 13, 13, 1, 1, 2, 1, 1] 100 rigid atoms, others: [1, 36, 37, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586913498 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 Building ZINC001586913498 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586913498 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 66) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001586913498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586913498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586913498 none O=C(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 6, 14, 14, 14, 14, 26, 26, 26, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 14, 14, 14, 14, 1, 1, 2, 1, 1] 100 rigid atoms, others: [1, 36, 37, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 67) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001586913498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586913498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586913498 none O=C(N1CCN(S(=O)(=O)c2ccc(Br)s2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 7, 13, 13, 13, 13, 25, 25, 25, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 13, 13, 13, 13, 1, 1, 2, 1, 1] 100 rigid atoms, others: [1, 36, 37, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586913498 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586913498 Building ZINC001586927041 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586927041 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/68 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/68' -> `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)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586927041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586927041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586927041 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 19, 21, 22, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 19, 19, 21, 21, 22, 37, 37, 37, 37, 37, 37] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/69 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/69' -> `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)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586927041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586927041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586927041 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 6, 6, 6, 19, 21, 22, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 19, 19, 21, 21, 22, 38, 38, 38, 38, 38, 38] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586927041 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 Building ZINC001586927041 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586927041 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 68) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586927041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586927041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586927041 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 19, 21, 22, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 19, 19, 21, 21, 22, 37, 37, 37, 37, 37, 37] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 69) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586927041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586927041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586927041 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 6, 6, 6, 19, 21, 22, 34, 34, 34, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 19, 19, 21, 21, 22, 38, 38, 38, 38, 38, 38] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001586927041 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001586927041 Building ZINC001587251435 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587251435 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/70 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1Cl) `ZINC001587251435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587251435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587251435 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 15, 15, 15, 15, 23, 23, 24, 30, 30, 30, 30, 26, 15, 15, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 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, 47, 48, 49, 50]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/71 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1Cl) `ZINC001587251435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587251435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587251435 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 16, 16, 12, 16, 24, 24, 25, 30, 30, 30, 30, 27, 16, 16, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001587251435 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 Building ZINC001587251435 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587251435 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 70) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1Cl) `ZINC001587251435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587251435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587251435 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 15, 15, 15, 15, 23, 23, 24, 30, 30, 30, 30, 26, 15, 15, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 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, 47, 48, 49, 50]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 71) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1Cl) `ZINC001587251435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587251435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587251435 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(S(=O)(=O)N3CCOCC3)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 16, 16, 12, 16, 24, 24, 25, 30, 30, 30, 30, 27, 16, 16, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001587251435 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001587251435 Building ZINC001595181057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595181057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/72 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21) `ZINC001595181057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595181057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001595181057 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 5, 5, 5, 9, 9, 9, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 1, 20, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 8, 9, 10, 11, 12, 3, 41, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 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/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/73 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21) `ZINC001595181057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595181057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001595181057 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 14, 15, 15, 14, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 14, 14, 15, 15, 14, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595181057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 Building ZINC001595181057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595181057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 72) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21) `ZINC001595181057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595181057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001595181057 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 5, 5, 5, 9, 9, 9, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 1, 20, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 8, 9, 10, 11, 12, 3, 41, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 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/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 73) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21) `ZINC001595181057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595181057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001595181057 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OCc2ccccc2)C[C@@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 14, 15, 15, 14, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 14, 14, 15, 15, 14, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595181057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595181057 Building ZINC001595684490 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595684490 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/74 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595684490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684490 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 16, 24, 24, 25, 25, 25, 25, 25, 25, 25, 24, 26, 26, 26, 26, 2, 2, 2, 2, 6, 6, 2, 3, 16, 16, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/75 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595684490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684490 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 8, 8, 4, 3, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595684490 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 Building ZINC001595684490 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595684490 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 74) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595684490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684490 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 16, 24, 24, 25, 25, 25, 25, 25, 25, 25, 24, 26, 26, 26, 26, 2, 2, 2, 2, 6, 6, 2, 3, 16, 16, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 75) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595684490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684490 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 8, 8, 4, 3, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595684490 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684490 Building ZINC001595684491 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595684491 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/76 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595684491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684491 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 10, 10, 4, 3, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/77 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595684491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684491 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 16, 22, 22, 23, 23, 23, 22, 23, 23, 23, 22, 24, 24, 24, 24, 2, 2, 2, 2, 6, 6, 2, 3, 16, 16, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595684491 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 Building ZINC001595684491 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595684491 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 76) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595684491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684491 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 10, 10, 4, 3, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 77) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1) `ZINC001595684491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595684491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001595684491 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(F)cccc1Cl)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 16, 22, 22, 23, 23, 23, 22, 23, 23, 23, 22, 24, 24, 24, 24, 2, 2, 2, 2, 6, 6, 2, 3, 16, 16, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/194367/xbs-8058088.45/working/building/ZINC001595684491 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595684491 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595684491 Building ZINC001595719984 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595719984 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/78 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/78' -> `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)N1CCCS(=O)(=O)C[C@H]1c1cnn(C)c1) `ZINC001595719984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595719984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719984 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/79 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/79' -> `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)N1CCCS(=O)(=O)C[C@H]1c1cnn(C)c1) `ZINC001595719984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595719984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719984 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 3, 3, 1, 1, 1, 1, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 3, 3, 3, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595719984 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 Building ZINC001595719984 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595719984 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 78) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@H]1c1cnn(C)c1) `ZINC001595719984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595719984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719984 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 79) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@H]1c1cnn(C)c1) `ZINC001595719984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595719984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719984 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 3, 3, 1, 1, 1, 1, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 3, 3, 3, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595719984 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719984 Building ZINC001595719985 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595719985 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/80 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/80' -> `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)N1CCCS(=O)(=O)C[C@@H]1c1cnn(C)c1) `ZINC001595719985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595719985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719985 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 1, 1, 1, 1, 9, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/81 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/81' -> `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)N1CCCS(=O)(=O)C[C@@H]1c1cnn(C)c1) `ZINC001595719985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595719985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719985 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 4, 11, 11, 3, 3, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 3, 3, 3, 11, 11, 11, 11, 11, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595719985 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 Building ZINC001595719985 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595719985 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 80) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@@H]1c1cnn(C)c1) `ZINC001595719985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595719985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719985 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 1, 1, 1, 1, 9, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 81) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@@H]1c1cnn(C)c1) `ZINC001595719985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595719985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001595719985 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCS(=O)(=O)C[C@@H]1c1cnn(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.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', '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'] 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, 11, 11, 5, 5, 7, 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] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 4, 11, 11, 3, 3, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 3, 3, 3, 11, 11, 11, 11, 11, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001595719985 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001595719985 Building ZINC001597577131 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577131 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/82 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577131 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 10, 26, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 10, 10, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/83 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577131 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 13, 30, 13, 13, 13, 13, 13, 13, 8, 13, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 13, 13, 13, 13, 8, 8, 8, 8, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577131 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 Building ZINC001597577131 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577131 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 82) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577131 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 10, 26, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 10, 10, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 83) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577131 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 13, 30, 13, 13, 13, 13, 13, 13, 8, 13, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 13, 13, 13, 13, 8, 8, 8, 8, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577131 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577131 Building ZINC001597577132 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577132 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/84 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577132 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 14, 32, 14, 14, 14, 14, 14, 14, 8, 14, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 14, 14, 8, 8, 8, 8, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14] 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/85 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577132 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 10, 26, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577132 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 Building ZINC001597577132 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577132 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 84) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577132 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 14, 32, 14, 14, 14, 14, 14, 14, 8, 14, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 14, 14, 8, 8, 8, 8, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14] 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 85) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001597577132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001597577132 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 10, 26, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577132 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577132 Building ZINC001597577625 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577625 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/86 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577625 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 26, 19, 26, 19, 19, 19, 19, 19, 19, 9, 19, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 19, 19, 9, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/87 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577625 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 31, 27, 19, 27, 19, 19, 19, 19, 19, 19, 14, 19, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 19, 14, 14, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577625 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 Building ZINC001597577625 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577625 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 86) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577625 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 26, 19, 26, 19, 19, 19, 19, 19, 19, 9, 19, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 19, 19, 9, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 87) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577625 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 31, 27, 19, 27, 19, 19, 19, 19, 19, 19, 14, 19, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 19, 14, 14, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577625 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577625 Building ZINC001597577626 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577626 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/88 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577626 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 25, 17, 25, 17, 17, 17, 17, 17, 17, 13, 17, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 17, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/89 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577626 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 26, 19, 26, 19, 19, 19, 19, 19, 19, 9, 18, 9, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 19, 19, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577626 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 Building ZINC001597577626 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597577626 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 88) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597577626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577626 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 25, 17, 25, 17, 17, 17, 17, 17, 17, 13, 17, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 17, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 89) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001597577626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597577626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001597577626 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=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', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 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, 6, 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, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 26, 19, 26, 19, 19, 19, 19, 19, 19, 9, 18, 9, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 19, 19, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597577626 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597577626 Building ZINC001597688933 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597688933 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/90 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl) `ZINC001597688933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597688933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001597688933 none COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 11, 4, 2, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 20, 20, 6, 2, 1, 4, 4, 1, 1, 1, 1, 6] 50 rigid atoms, others: [43, 37, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 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/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/91 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl) `ZINC001597688933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597688933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001597688933 none COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 7, 5, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 21, 21, 21, 21, 21, 20, 20, 7, 2, 1, 4, 4, 1, 1, 1, 1, 7] 50 rigid atoms, others: [43, 37, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 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/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597688933 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 Building ZINC001597688933 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597688933 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 90) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl) `ZINC001597688933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597688933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001597688933 none COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 11, 4, 2, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 20, 20, 6, 2, 1, 4, 4, 1, 1, 1, 1, 6] 50 rigid atoms, others: [43, 37, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 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/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 91) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl) `ZINC001597688933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597688933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001597688933 none COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 7, 5, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 21, 21, 21, 21, 21, 20, 20, 7, 2, 1, 4, 4, 1, 1, 1, 1, 7] 50 rigid atoms, others: [43, 37, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 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/194367/xbs-8058088.45/working/building/ZINC001597688933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001597688933 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001597688933 Building ZINC001598091580 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598091580 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/92 `/scratch/xiaobo/194367/xbs-8058088.45/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)NCc1nnc2c(=O)[nH]ccn12) `ZINC001598091580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598091580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001598091580 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nnc2c(=O)[nH]ccn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/93 `/scratch/xiaobo/194367/xbs-8058088.45/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)NCc1nnc2c(=O)[nH]ccn12) `ZINC001598091580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598091580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001598091580 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nnc2c(=O)[nH]ccn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001598091580 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 Building ZINC001598091580 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598091580 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 92) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)NCc1nnc2c(=O)[nH]ccn12) `ZINC001598091580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598091580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001598091580 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nnc2c(=O)[nH]ccn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 93) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)NCc1nnc2c(=O)[nH]ccn12) `ZINC001598091580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598091580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001598091580 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nnc2c(=O)[nH]ccn12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 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, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001598091580 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001598091580 Building ZINC001631641923 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641923 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/94 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641923 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 17, 17, 17, 17, 17, 17, 17, 17, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 18, 18, 18, 17, 17, 17, 17, 8, 8, 8, 3, 4, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/95 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641923 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 6, 20, 20, 20, 20, 20, 20, 20, 20, 2, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 21, 21, 21, 20, 20, 20, 20, 6, 6, 6, 2, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641923 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 Building ZINC001631641923 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641923 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 94) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641923 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 17, 17, 17, 17, 17, 17, 17, 17, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 18, 18, 18, 17, 17, 17, 17, 8, 8, 8, 3, 4, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 95) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641923 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 6, 20, 20, 20, 20, 20, 20, 20, 20, 2, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 21, 21, 21, 20, 20, 20, 20, 6, 6, 6, 2, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641923 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641923 Building ZINC001631641924 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641924 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/96 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641924 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 21, 21, 21, 21, 21, 21, 21, 21, 2, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 22, 22, 22, 21, 21, 21, 21, 7, 7, 7, 2, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/97 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641924 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 16, 16, 16, 16, 16, 16, 16, 16, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 17, 17, 17, 16, 16, 16, 16, 8, 8, 8, 3, 4, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641924 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 Building ZINC001631641924 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641924 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 96) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641924 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 21, 21, 21, 21, 21, 21, 21, 21, 2, 7, 7, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 22, 22, 22, 21, 21, 21, 21, 7, 7, 7, 2, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 97) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641924 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 16, 16, 16, 16, 16, 16, 16, 16, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 17, 17, 17, 16, 16, 16, 16, 8, 8, 8, 3, 4, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641924 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641924 Building ZINC001631641925 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641925 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/98 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641925 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 16, 16, 16, 16, 16, 16, 16, 16, 4, 12, 12, 4, 1, 4, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 18, 18, 18, 16, 16, 16, 16, 12, 12, 12, 4, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/99 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641925 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 11, 14, 14, 14, 14, 14, 14, 14, 14, 3, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 16, 16, 16, 14, 14, 14, 14, 11, 11, 11, 3, 4, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641925 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 Building ZINC001631641925 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641925 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 98) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641925 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 16, 16, 16, 16, 16, 16, 16, 16, 4, 12, 12, 4, 1, 4, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 18, 18, 18, 16, 16, 16, 16, 12, 12, 12, 4, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 99) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641925 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 11, 14, 14, 14, 14, 14, 14, 14, 14, 3, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 16, 16, 16, 14, 14, 14, 14, 11, 11, 11, 3, 4, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641925 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641925 Building ZINC001631641926 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641926 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/100 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641926 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 11, 14, 14, 14, 14, 14, 14, 14, 14, 3, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 15, 15, 15, 14, 14, 14, 14, 11, 11, 11, 3, 4, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/101 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641926 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 16, 16, 16, 16, 16, 16, 16, 16, 4, 12, 12, 4, 1, 4, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 18, 18, 18, 16, 16, 16, 16, 12, 12, 12, 4, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641926 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 Building ZINC001631641926 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631641926 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 100) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631641926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641926 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 11, 14, 14, 14, 14, 14, 14, 14, 14, 3, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 15, 15, 15, 14, 14, 14, 14, 11, 11, 11, 3, 4, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 101) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631641926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631641926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001631641926 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 16, 16, 16, 16, 16, 16, 16, 16, 4, 12, 12, 4, 1, 4, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 18, 18, 18, 16, 16, 16, 16, 12, 12, 12, 4, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631641926 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631641926 Building ZINC001631995568 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631995568 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/102 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1) `ZINC001631995568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631995568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631995568 none COc1ccc(S(=O)(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 50, 50, 38, 21, 38, 38, 21, 21, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 3, 3, 21, 21, 50, 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, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/103 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CC(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1) `ZINC001631995568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631995568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631995568 none COc1ccc(S(=O)(=O)N2CC(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 33, 48, 48, 33, 18, 33, 33, 18, 18, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 18, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 2, 5, 5, 18, 18, 48, 48] 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: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631995568 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 Building ZINC001631995568 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631995568 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 102) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(S(=O)(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1) `ZINC001631995568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631995568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631995568 none COc1ccc(S(=O)(=O)N2CC(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 50, 50, 38, 21, 38, 38, 21, 21, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 3, 3, 21, 21, 50, 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, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 103) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(S(=O)(=O)N2CC(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1) `ZINC001631995568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631995568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631995568 none COc1ccc(S(=O)(=O)N2CC(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 33, 48, 48, 33, 18, 33, 33, 18, 18, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 18, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 2, 5, 5, 18, 18, 48, 48] 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: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001631995568 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001631995568 Building ZINC001632176972 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632176972 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/104 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br) `ZINC001632176972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632176972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001632176972 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'N.ar', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/105 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br) `ZINC001632176972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632176972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001632176972 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'N.ar', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001632176972 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 Building ZINC001632176972 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632176972 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 104) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br) `ZINC001632176972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632176972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001632176972 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'N.ar', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 105) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br) `ZINC001632176972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632176972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001632176972 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc2cccnc2cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'N.ar', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001632176972 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001632176972 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632176972 Building ZINC001632554050 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632554050 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/106 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001632554050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632554050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632554050 none COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 31, 32, 32, 32, 18, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 32, 32, 32, 32, 32, 32, 18, 18, 18, 18, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 40, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/107 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001632554050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632554050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632554050 none COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 18, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 33, 33, 33, 32, 32, 32, 18, 18, 18, 18, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 40, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001632554050 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 Building ZINC001632554050 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632554050 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 106) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001632554050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632554050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632554050 none COc1cc(Br)ccc1CCCNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 31, 32, 32, 32, 18, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 32, 32, 32, 32, 32, 32, 18, 18, 18, 18, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 40, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 107) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001632554050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632554050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632554050 none COc1cc(Br)ccc1CCCNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 18, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 33, 33, 33, 32, 32, 32, 18, 18, 18, 18, 12, 12, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [45, 40, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001632554050 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632554050 Building ZINC001632823664 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632823664 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/108 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC001632823664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632823664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001632823664 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 27, 27, 27, 27, 27, 27, 27, 18, 7, 7, 5, 5, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 27, 27] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/109 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC001632823664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632823664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001632823664 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 26, 8, 6, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 26, 26, 26, 26, 26, 26, 26, 19, 8, 8, 6, 6, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001632823664 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 Building ZINC001632823664 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632823664 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 108) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC001632823664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632823664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001632823664 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 27, 7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 27, 27, 27, 27, 27, 27, 27, 18, 7, 7, 5, 5, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 27, 27] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 109) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC001632823664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632823664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001632823664 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 26, 8, 6, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 26, 26, 26, 26, 26, 26, 26, 19, 8, 8, 6, 6, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001632823664 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001632823664 Building ZINC001633121329 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121329 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/110 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/111 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/112 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/112' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/113 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/113' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121329 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 Building ZINC001633121329 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121329 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 110) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 111) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 112) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 113) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121329 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 Building ZINC001633121329 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121329 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 110) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 111) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 112) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 113) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121329 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 Building ZINC001633121329 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121329 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 110) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 111) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 112) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 113) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121329.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121329 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121329 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121329 Building ZINC001633121330 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121330 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/114 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/115 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/116 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/116' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/117 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/117' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121330 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 Building ZINC001633121330 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121330 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 114) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 115) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 116) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 117) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121330 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 Building ZINC001633121330 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121330 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 114) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 115) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 116) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 117) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121330 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 Building ZINC001633121330 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121330 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 114) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 115) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 116) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 6, 6, 3, 2, 11, 11, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 117) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001633121330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121330 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121330 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121330 Building ZINC001633121331 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121331 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/118 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/119 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/120 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/120' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/121 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/121' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121331 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 Building ZINC001633121331 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121331 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 118) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 119) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 120) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 121) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121331 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 Building ZINC001633121331 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121331 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 118) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 119) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 120) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 121) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121331 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 Building ZINC001633121331 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121331 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 118) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 119) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 120) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 6, 6, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 121) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121331.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121331 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121331 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121331 Building ZINC001633121332 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121332 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/122 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/123 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/124 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/124' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/125 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/125' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121332 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 Building ZINC001633121332 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121332 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 122) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 123) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 124) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 125) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121332 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 Building ZINC001633121332 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121332 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 122) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 123) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 124) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 125) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121332 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 Building ZINC001633121332 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633121332 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 122) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 123) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 124) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 125) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001633121332.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633121332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001633121332 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001633121332 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633121332 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633121332 Building ZINC001633359771 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633359771 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/126 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633359771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359771 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 20, 10, 16, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20, 10, 10, 2, 2, 5, 5, 2, 2, 2, 2, 16, 16, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/127 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633359771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359771 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 21, 12, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 12, 12, 2, 2, 5, 5, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633359771 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 Building ZINC001633359771 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633359771 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 126) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633359771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359771 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 20, 10, 16, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20, 10, 10, 2, 2, 5, 5, 2, 2, 2, 2, 16, 16, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 127) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633359771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359771 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 21, 12, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 12, 12, 2, 2, 5, 5, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633359771 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359771 Building ZINC001633359775 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633359775 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/128 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633359775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359775 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 21, 12, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 12, 12, 2, 2, 5, 5, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/129 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633359775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359775 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 20, 10, 16, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20, 10, 10, 2, 2, 5, 5, 2, 2, 2, 2, 16, 16, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633359775 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 Building ZINC001633359775 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633359775 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 128) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633359775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359775 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 21, 12, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 12, 12, 2, 2, 5, 5, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 129) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21) `ZINC001633359775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633359775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001633359775 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 20, 10, 16, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20, 10, 10, 2, 2, 5, 5, 2, 2, 2, 2, 16, 16, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633359775 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633359775 Building ZINC001633531469 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633531469 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/130 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633531469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531469 none CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 14, 14, 7, 14, 14, 14, 14, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 7, 7, 8, 8, 8, 8, 8, 14, 14, 14, 7, 7, 7, 7, 2, 7, 7, 2, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/131 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633531469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531469 none CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 13, 13, 8, 13, 13, 13, 13, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8, 8, 8, 2, 7, 7, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633531469 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 Building ZINC001633531469 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633531469 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 130) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633531469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531469 none CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 14, 14, 7, 14, 14, 14, 14, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 7, 7, 8, 8, 8, 8, 8, 14, 14, 14, 7, 7, 7, 7, 2, 7, 7, 2, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 131) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633531469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531469 none CC[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 13, 13, 8, 13, 13, 13, 13, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8, 8, 8, 2, 7, 7, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633531469 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531469 Building ZINC001633531471 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633531471 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/132 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633531471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531471 none CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 16, 16, 14, 16, 16, 16, 16, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 8, 8, 12, 12, 12, 12, 12, 16, 16, 16, 8, 8, 8, 8, 2, 7, 7, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/133 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633531471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531471 none CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 8, 8, 9, 9, 9, 9, 9, 15, 15, 15, 8, 8, 8, 8, 2, 6, 6, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633531471 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 Building ZINC001633531471 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633531471 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 132) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633531471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531471 none CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 16, 16, 14, 16, 16, 16, 16, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 8, 8, 12, 12, 12, 12, 12, 16, 16, 16, 8, 8, 8, 8, 2, 7, 7, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 133) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001633531471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633531471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001633531471 none CC[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 8, 8, 9, 9, 9, 9, 9, 15, 15, 15, 8, 8, 8, 8, 2, 6, 6, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633531471 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633531471 Building ZINC001633883777 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633883777 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/134 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1) `ZINC001633883777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633883777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633883777 none COc1cccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 2, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 22] 50 rigid atoms, others: [45, 39, 44, 10, 43, 12, 13, 14, 15, 16, 17, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/135 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1) `ZINC001633883777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633883777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633883777 none COc1cccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 2, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 21] 50 rigid atoms, others: [45, 39, 44, 10, 43, 12, 13, 14, 15, 16, 17, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633883777 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 Building ZINC001633883777 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633883777 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 134) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1) `ZINC001633883777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633883777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633883777 none COc1cccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 2, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 22] 50 rigid atoms, others: [45, 39, 44, 10, 43, 12, 13, 14, 15, 16, 17, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 135) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1) `ZINC001633883777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633883777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633883777 none COc1cccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 2, 1, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 21] 50 rigid atoms, others: [45, 39, 44, 10, 43, 12, 13, 14, 15, 16, 17, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633883777 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633883777 Building ZINC001633898655 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633898655 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/136 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1) `ZINC001633898655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633898655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633898655 none COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 12, 12, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 3, 5, 12, 12, 5, 5, 5, 5, 7, 7, 7, 7, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/137 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1) `ZINC001633898655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633898655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633898655 none COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 16, 16, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 4, 4, 11, 11, 4, 4, 4, 4, 8, 8, 8, 8, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633898655 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 Building ZINC001633898655 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633898655 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 136) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1) `ZINC001633898655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633898655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633898655 none COc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 12, 12, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 3, 5, 12, 12, 5, 5, 5, 5, 7, 7, 7, 7, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 137) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1) `ZINC001633898655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633898655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001633898655 none COc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3ccccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 16, 16, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 4, 4, 11, 11, 4, 4, 4, 4, 8, 8, 8, 8, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001633898655 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001633898655 Building ZINC001634185488 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634185488 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/138 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/139 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/140 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/140' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/141 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/141' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634185488 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 Building ZINC001634185488 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634185488 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 138) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 139) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 140) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 141) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634185488 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 Building ZINC001634185488 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634185488 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 138) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 139) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 140) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 141) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634185488 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 Building ZINC001634185488 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634185488 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 138) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 139) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 140) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 141) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1) `ZINC001634185488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634185488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001634185488 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2ccccc2)C2(CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 2, 7, 11, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 6, 6, 2, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634185488 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634185488 Building ZINC001634571887 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634571887 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/142 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/142' -> `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(S(N)(=O)=O)cn1C) `ZINC001634571887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634571887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571887 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 16, 2, 7, 7, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 20, 20, 20, 20, 20, 16, 16, 17, 17, 17, 17, 17, 17, 17, 2, 3, 6, 6, 3, 3, 3, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/143 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/143' -> `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(S(N)(=O)=O)cn1C) `ZINC001634571887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634571887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571887 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 14, 6, 14, 2, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634571887 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 Building ZINC001634571887 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634571887 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 142) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001634571887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634571887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571887 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 16, 2, 7, 7, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 20, 20, 20, 20, 20, 16, 16, 17, 17, 17, 17, 17, 17, 17, 2, 3, 6, 6, 3, 3, 3, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 143) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001634571887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634571887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571887 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 14, 6, 14, 2, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634571887 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571887 Building ZINC001634571888 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634571888 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/144 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/144' -> `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(S(N)(=O)=O)cn1C) `ZINC001634571888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634571888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571888 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 15, 2, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 22, 22, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/145 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/145' -> `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(S(N)(=O)=O)cn1C) `ZINC001634571888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634571888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571888 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 16, 2, 7, 7, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 20, 20, 20, 20, 20, 15, 15, 16, 16, 16, 16, 16, 16, 16, 2, 3, 6, 6, 3, 3, 3, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634571888 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 Building ZINC001634571888 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634571888 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 144) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001634571888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634571888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571888 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 15, 2, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 22, 22, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 145) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001634571888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634571888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634571888 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 7, 16, 2, 7, 7, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 20, 20, 20, 20, 20, 15, 15, 16, 16, 16, 16, 16, 16, 16, 2, 3, 6, 6, 3, 3, 3, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634571888 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634571888 Building ZINC001634929987 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634929987 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/146 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929987 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 4, 4, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 3, 10, 10, 3, 4, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/147 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929987 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 4, 1, 1, 1, 1, 4, 4, 5, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 4, 4, 4, 4, 15, 15, 4, 4, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634929987 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 Building ZINC001634929987 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634929987 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 146) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929987 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 4, 4, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 3, 10, 10, 3, 4, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 147) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634929987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929987 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 4, 1, 1, 1, 1, 4, 4, 5, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 4, 4, 4, 4, 15, 15, 4, 4, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/194367/xbs-8058088.45/working/building/ZINC001634929987 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634929987 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929987 Building ZINC001634929988 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634929988 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/148 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634929988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929988 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 4, 1, 1, 1, 1, 4, 4, 6, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 4, 4, 4, 4, 15, 15, 4, 4, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/149 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634929988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929988 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 4, 4, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 3, 10, 10, 3, 4, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634929988 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 Building ZINC001634929988 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634929988 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 148) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634929988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929988 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 4, 1, 1, 1, 1, 4, 4, 6, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 4, 4, 4, 4, 15, 15, 4, 4, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 149) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1) `ZINC001634929988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634929988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001634929988 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 4, 4, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 3, 3, 3, 3, 10, 10, 3, 4, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634929988 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634929988 Building ZINC001635011873 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635011873 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/150 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635011873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011873 none CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 20, 17, 19, 8, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/151 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635011873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011873 none CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 12, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001635011873 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 Building ZINC001635011873 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635011873 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 150) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635011873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011873 none CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 20, 17, 19, 8, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 151) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635011873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011873 none CC1CCN(C(=O)OC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 12, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001635011873 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011873 Building ZINC001635011874 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635011874 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/152 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635011874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011874 none CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 16, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 22, 22, 22, 22] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/153 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635011874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011874 none CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 9, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001635011874 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 Building ZINC001635011874 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635011874 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 152) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635011874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011874 none CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 16, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 22, 22, 22, 22] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 153) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001635011874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635011874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635011874 none CC1CCN(C(=O)OC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 9, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 1, 1, 1, 1, 24, 24, 24, 24] 50 rigid atoms, others: [54, 55, 50, 16, 18, 19, 20, 21, 22, 23, 56, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001635011874 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635011874 Building ZINC001635320155 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635320155 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/154 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2) `ZINC001635320155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635320155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001635320155 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 1, 11, 5, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 11, 20, 20, 24, 24, 24, 20, 20, 20, 20, 2, 2, 2, 2, 6, 6, 2, 3, 20, 20, 20, 24, 24, 24, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/155 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2) `ZINC001635320155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635320155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001635320155 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 1, 11, 5, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 11, 20, 20, 25, 25, 25, 20, 20, 20, 20, 2, 2, 2, 2, 6, 6, 2, 3, 20, 20, 20, 25, 25, 25, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 130 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001635320155 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 Building ZINC001635320155 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635320155 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 154) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2) `ZINC001635320155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635320155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001635320155 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 1, 11, 5, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 11, 20, 20, 24, 24, 24, 20, 20, 20, 20, 2, 2, 2, 2, 6, 6, 2, 3, 20, 20, 20, 24, 24, 24, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 155) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2) `ZINC001635320155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635320155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001635320155 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)N(CC(F)F)C(=O)CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 1, 11, 5, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 1, 3, 3, 3, 11, 20, 20, 20, 11, 20, 20, 25, 25, 25, 20, 20, 20, 20, 2, 2, 2, 2, 6, 6, 2, 3, 20, 20, 20, 25, 25, 25, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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: 130 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001635320155 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001635320155 Building ZINC001636081810 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636081810 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/156 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1) `ZINC001636081810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636081810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001636081810 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 18, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 11, 11, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/157 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1) `ZINC001636081810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636081810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001636081810 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 18, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 11, 11, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001636081810 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 Building ZINC001636081810 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636081810 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 156) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1) `ZINC001636081810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636081810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001636081810 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 18, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 11, 11, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 157) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1) `ZINC001636081810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636081810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001636081810 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1cc(F)cc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 18, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 11, 11, 18, 18, 26, 26, 26, 26, 26, 26, 26, 18] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001636081810 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636081810 Building ZINC001636584667 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636584667 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/158 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001636584667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636584667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636584667 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 27, 27, 16, 9, 16, 9, 9, 9, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 4, 6, 6, 4, 6, 6, 4, 9, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/159 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001636584667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636584667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636584667 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 27, 13, 7, 13, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 6, 8, 8, 6, 8, 8, 6, 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, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001636584667 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 Building ZINC001636584667 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636584667 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 158) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001636584667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636584667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636584667 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 27, 27, 16, 9, 16, 9, 9, 9, 8, 2, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 4, 6, 6, 4, 6, 6, 4, 9, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 159) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001636584667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636584667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636584667 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 27, 13, 7, 13, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 6, 8, 8, 6, 8, 8, 6, 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, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001636584667 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001636584667 Building ZINC001637253642 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637253642 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/160 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1) `ZINC001637253642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637253642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637253642 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 1, 1, 1, 1, 4, 4, 1, 7, 7, 7, 7, 7, 23, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 35, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/161 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1) `ZINC001637253642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637253642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637253642 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 4, 4, 1, 6, 6, 6, 6, 6, 21, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 35, 29, 30, 31] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001637253642 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 Building ZINC001637253642 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637253642 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 160) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1) `ZINC001637253642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637253642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637253642 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 1, 1, 1, 1, 4, 4, 1, 7, 7, 7, 7, 7, 23, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 35, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 161) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1) `ZINC001637253642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637253642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637253642 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(C(F)(F)F)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 4, 4, 1, 6, 6, 6, 6, 6, 21, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 35, 29, 30, 31] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001637253642 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637253642 Building ZINC001637979452 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637979452 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/162 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1) `ZINC001637979452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637979452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001637979452 none CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.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, 14, 11, 11, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 15, 15, 19, 19, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 19, 19, 36, 36, 36, 36, 19, 19, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/163 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1) `ZINC001637979452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637979452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001637979452 none CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.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, 14, 11, 11, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 34, 16, 16, 19, 19, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 19, 19, 34, 34, 34, 33, 19, 19, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001637979452 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 Building ZINC001637979452 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637979452 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 162) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1) `ZINC001637979452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637979452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001637979452 none CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.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, 14, 11, 11, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 15, 15, 19, 19, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 19, 19, 36, 36, 36, 36, 19, 19, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 163) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1) `ZINC001637979452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637979452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001637979452 none CS(=O)(=O)Nc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.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, 14, 11, 11, 8, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 34, 16, 16, 19, 19, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 19, 19, 34, 34, 34, 33, 19, 19, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001637979452 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001637979452 Building ZINC001638122520 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638122520 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/164 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/165 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/166 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/166' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/167 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/167' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638122520 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 Building ZINC001638122520 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638122520 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 164) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 165) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 166) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 167) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638122520 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 Building ZINC001638122520 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638122520 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 164) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 165) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 166) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 167) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638122520 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 Building ZINC001638122520 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001638122520 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 164) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 165) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 166) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 167) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O) `ZINC001638122520.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001638122520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001638122520 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 19, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 13, 13, 7, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 19, 19, 32, 32, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638122520 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638122520 Building ZINC001638325876 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638325876 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/168 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001638325876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638325876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001638325876 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 2, 4, 7, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/169 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001638325876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638325876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001638325876 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 2, 4, 8, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638325876 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 Building ZINC001638325876 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638325876 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 168) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001638325876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638325876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001638325876 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 2, 4, 7, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 169) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001638325876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638325876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001638325876 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations 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, 2, 4, 8, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638325876 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638325876 Building ZINC001638388954 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638388954 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/170 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12) `ZINC001638388954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638388954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638388954 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/171 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12) `ZINC001638388954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638388954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638388954 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 11, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 18, 18, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638388954 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 Building ZINC001638388954 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638388954 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 170) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12) `ZINC001638388954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638388954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638388954 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 18, 18, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 171) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12) `ZINC001638388954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638388954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001638388954 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cccc(Br)c12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 11, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 18, 18, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001638388954 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001638388954 Building ZINC001639099165 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639099165 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/172 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/172' -> `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](CS(N)(=O)=O)C1) `ZINC001639099165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639099165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 9, 9, 9, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/173 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/173' -> `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](CS(N)(=O)=O)C1) `ZINC001639099165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639099165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 7, 12, 12, 12, 4, 2, 2, 2, 16, 16, 6, 16, 2, 2, 2, 4, 4, 4, 4, 7, 7, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639099165 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 Building ZINC001639099165 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639099165 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 172) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CS(N)(=O)=O)C1) `ZINC001639099165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639099165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 9, 9, 9, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 173) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CS(N)(=O)=O)C1) `ZINC001639099165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639099165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099165 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 7, 12, 12, 12, 4, 2, 2, 2, 16, 16, 6, 16, 2, 2, 2, 4, 4, 4, 4, 7, 7, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639099165 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099165 Building ZINC001639099166 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639099166 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/174 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/174' -> `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](CS(N)(=O)=O)C1) `ZINC001639099166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639099166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099166 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 6, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 7, 11, 11, 11, 4, 2, 2, 2, 16, 16, 7, 16, 2, 2, 2, 4, 4, 4, 4, 7, 7, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/175 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/175' -> `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](CS(N)(=O)=O)C1) `ZINC001639099166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639099166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099166 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 2, 2, 2, 6, 9, 9, 9, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639099166 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 Building ZINC001639099166 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639099166 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 174) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CS(N)(=O)=O)C1) `ZINC001639099166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639099166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099166 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 6, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 7, 11, 11, 11, 4, 2, 2, 2, 16, 16, 7, 16, 2, 2, 2, 4, 4, 4, 4, 7, 7, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 175) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CS(N)(=O)=O)C1) `ZINC001639099166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639099166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639099166 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 2, 2, 2, 6, 9, 9, 9, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639099166 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639099166 Building ZINC001639575907 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575907 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/176 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/177 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/178 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/178' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/179 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/179' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575907 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 Building ZINC001639575907 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575907 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 176) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 177) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 178) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 179) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575907 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 Building ZINC001639575907 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575907 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 176) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 177) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 178) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 179) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575907 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 Building ZINC001639575907 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575907 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 176) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 177) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 178) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 24, 24, 23, 24, 24, 24, 12, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 179) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575907 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575907 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575907 Building ZINC001639575910 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575910 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/180 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/181 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/182 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/182' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/183 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/183' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575910 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 Building ZINC001639575910 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575910 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 180) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 181) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 182) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 183) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575910 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 Building ZINC001639575910 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575910 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 180) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 181) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 182) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 183) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575910 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 Building ZINC001639575910 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001639575910 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 180) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 181) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 182) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 183) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1) `ZINC001639575910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001639575910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001639575910 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(c2cccc(Br)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 22, 22, 22, 22, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 34, 28, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001639575910 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001639575910 Building ZINC001640255481 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640255481 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/184 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1) `ZINC001640255481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640255481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001640255481 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 6, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 20, 20, 20, 20, 20, 7, 7, 7, 4, 4, 4, 4, 14, 14, 4, 3, 7, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/185 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1) `ZINC001640255481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640255481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001640255481 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 6, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 19, 19, 19, 19, 19, 7, 7, 7, 4, 4, 4, 4, 14, 14, 4, 3, 7, 19, 19] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001640255481 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 Building ZINC001640255481 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640255481 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 184) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1) `ZINC001640255481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640255481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001640255481 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 6, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 20, 20, 20, 20, 20, 7, 7, 7, 4, 4, 4, 4, 14, 14, 4, 3, 7, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 185) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1) `ZINC001640255481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640255481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001640255481 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccc(Br)s2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 6, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 19, 19, 19, 19, 19, 7, 7, 7, 4, 4, 4, 4, 14, 14, 4, 3, 7, 19, 19] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001640255481 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640255481 Building ZINC001640283195 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640283195 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/186 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1) `ZINC001640283195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640283195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001640283195 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 2, 4, 9, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 1, 1, 1, 1, 4, 4, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 2, 35, 4] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/187 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1) `ZINC001640283195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640283195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001640283195 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 2, 4, 9, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 2, 2, 2, 2, 5, 5, 2, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001640283195 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 Building ZINC001640283195 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640283195 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 186) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1) `ZINC001640283195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640283195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001640283195 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 2, 4, 9, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 1, 1, 1, 1, 4, 4, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 2, 35, 4] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 187) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1) `ZINC001640283195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640283195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001640283195 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCN(Cc3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 2, 4, 9, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 2, 2, 2, 2, 5, 5, 2, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001640283195 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001640283195 Building ZINC001641035222 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641035222 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/188 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F) `ZINC001641035222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641035222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641035222 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/189 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F) `ZINC001641035222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641035222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641035222 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641035222 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 Building ZINC001641035222 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641035222 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 188) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F) `ZINC001641035222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641035222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641035222 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 189) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F) `ZINC001641035222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641035222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641035222 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(I)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641035222 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641035222 Building ZINC001641171564 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641171564 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/190 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001641171564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641171564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001641171564 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', '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: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 6, 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: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 41, 29, 29, 29, 29, 6, 21, 6, 6, 6, 3, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 29, 29, 41, 41, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 2, 2, 6, 6, 6, 6, 29, 29, 29, 29] 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, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/191 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001641171564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641171564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001641171564 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', '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: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 6, 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: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 40, 28, 28, 28, 28, 5, 21, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 28, 28, 40, 40, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 28, 28, 28, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641171564 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 Building ZINC001641171564 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641171564 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 190) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001641171564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641171564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001641171564 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', '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: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 6, 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: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 41, 29, 29, 29, 29, 6, 21, 6, 6, 6, 3, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 29, 29, 41, 41, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 2, 2, 6, 6, 6, 6, 29, 29, 29, 29] 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, 46, 47, 48]) total number of confs: 113 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 191) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001641171564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641171564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001641171564 none NC(=O)C1CCN(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', '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: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 6, 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: [4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 40, 28, 28, 28, 28, 5, 21, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 28, 28, 40, 40, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 28, 28, 28, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641171564 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641171564 Building ZINC001641403672 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641403672 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/192 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403672 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 4, 10, 10, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 4, 11, 11, 11, 11, 4, 4, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4] 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/193 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403672 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 11, 3, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 3, 16, 16, 16, 16, 3, 3, 3, 3, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641403672 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 Building ZINC001641403672 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641403672 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 192) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403672 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 4, 10, 10, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 4, 11, 11, 11, 11, 4, 4, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4] 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 193) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641403672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403672 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 11, 3, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 3, 16, 16, 16, 16, 3, 3, 3, 3, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641403672 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403672 Building ZINC001641403673 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641403673 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/194 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641403673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403673 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 11, 3, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 15, 15, 15, 15, 3, 3, 3, 3, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/195 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641403673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403673 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 4, 10, 10, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 4, 11, 11, 11, 11, 4, 4, 4, 4, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 4, 4] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641403673 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 Building ZINC001641403673 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641403673 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 194) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641403673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403673 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 11, 3, 11, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 15, 15, 15, 15, 3, 3, 3, 3, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 195) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001641403673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641403673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641403673 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 4, 7, 6, 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] 0 hydrogens 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, 4, 10, 10, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 4, 11, 11, 11, 11, 4, 4, 4, 4, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 4, 4] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641403673 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641403673 Building ZINC001641433970 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641433970 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/196 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/196' -> `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)N1CCN(C(=O)[C@H](C)O)CC1) `ZINC001641433970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641433970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433970 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 5, 8, 12, 12, 11, 12, 14, 14, 14, 14, 14, 12, 12, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 12, 12, 12, 12, 14, 14, 14, 42, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/197 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/197' -> `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)N1CCN(C(=O)[C@H](C)O)CC1) `ZINC001641433970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641433970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433970 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 7, 7, 7, 7, 10, 10, 10, 30, 7, 7, 7, 7] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641433970 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 Building ZINC001641433970 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641433970 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 196) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H](C)O)CC1) `ZINC001641433970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641433970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433970 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 5, 8, 12, 12, 11, 12, 14, 14, 14, 14, 14, 12, 12, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 12, 12, 12, 12, 14, 14, 14, 42, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 197) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H](C)O)CC1) `ZINC001641433970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641433970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433970 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 7, 7, 7, 7, 10, 10, 10, 30, 7, 7, 7, 7] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641433970 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433970 Building ZINC001641433971 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641433971 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/198 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/198' -> `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)N1CCN(C(=O)[C@@H](C)O)CC1) `ZINC001641433971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641433971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433971 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7, 7, 7, 9, 9, 9, 27, 7, 7, 7, 7] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/199 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/199' -> `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)N1CCN(C(=O)[C@@H](C)O)CC1) `ZINC001641433971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641433971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433971 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 15, 15, 6, 15, 3, 3, 3, 6, 6, 6, 6, 10, 10, 10, 30, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641433971 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 Building ZINC001641433971 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641433971 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 198) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H](C)O)CC1) `ZINC001641433971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641433971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433971 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7, 7, 7, 9, 9, 9, 27, 7, 7, 7, 7] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 199) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H](C)O)CC1) `ZINC001641433971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641433971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641433971 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H](C)O)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 15, 15, 6, 15, 3, 3, 3, 6, 6, 6, 6, 10, 10, 10, 30, 6, 6, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 98 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641433971 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641433971 Building ZINC001641490544 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641490544 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/200 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1) `ZINC001641490544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641490544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490544 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 12, 10, 17, 20, 20, 20, 20, 20, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 12, 12, 36, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/201 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1) `ZINC001641490544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641490544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490544 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 14, 9, 13, 14, 14, 14, 14, 14, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 3, 14, 14, 42, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641490544 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 Building ZINC001641490544 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641490544 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 200) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1) `ZINC001641490544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641490544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490544 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 12, 10, 17, 20, 20, 20, 20, 20, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 12, 12, 36, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 201) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1) `ZINC001641490544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641490544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490544 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 14, 9, 13, 14, 14, 14, 14, 14, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 3, 14, 14, 42, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641490544 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490544 Building ZINC001641490545 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641490545 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/202 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1) `ZINC001641490545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641490545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490545 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 11, 7, 10, 11, 11, 11, 11, 11, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 3, 11, 11, 33, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/203 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1) `ZINC001641490545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641490545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490545 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 12, 10, 15, 18, 18, 18, 18, 18, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 3, 12, 12, 36, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641490545 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 Building ZINC001641490545 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641490545 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 202) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1) `ZINC001641490545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641490545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490545 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 11, 7, 10, 11, 11, 11, 11, 11, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 3, 11, 11, 33, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 203) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1) `ZINC001641490545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641490545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641490545 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 12, 10, 15, 18, 18, 18, 18, 18, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 3, 12, 12, 36, 15, 15, 18, 18, 18, 18, 18, 18, 18, 18] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641490545 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641490545 Building ZINC001641723633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641723633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/204 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/204' -> `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)CCOc1ccc(S(N)(=O)=O)cc1) `ZINC001641723633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641723633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001641723633 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1ccc(S(N)(=O)=O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.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'] 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, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 7, 8, 18, 22, 22, 18, 18, 35, 35, 35, 22, 22, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 22, 22, 35, 35, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/205 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/205' -> `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)CCOc1ccc(S(N)(=O)=O)cc1) `ZINC001641723633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641723633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001641723633 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1ccc(S(N)(=O)=O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.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'] 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, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 9, 18, 22, 22, 18, 18, 38, 38, 38, 22, 22, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 4, 4, 4, 8, 8, 9, 9, 22, 22, 38, 38, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641723633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 Building ZINC001641723633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641723633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 204) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1ccc(S(N)(=O)=O)cc1) `ZINC001641723633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641723633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001641723633 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1ccc(S(N)(=O)=O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.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'] 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, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 7, 8, 18, 22, 22, 18, 18, 35, 35, 35, 22, 22, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 22, 22, 35, 35, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 205) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1ccc(S(N)(=O)=O)cc1) `ZINC001641723633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641723633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001641723633 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1ccc(S(N)(=O)=O)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.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'] 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, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 8, 9, 18, 22, 22, 18, 18, 38, 38, 38, 22, 22, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 4, 4, 4, 8, 8, 9, 9, 22, 22, 38, 38, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001641723633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001641723633 Building ZINC001642000175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642000175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/206 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/206' -> `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)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001642000175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642000175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001642000175 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/207 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/207' -> `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)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001642000175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642000175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001642000175 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 9, 9, 9, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642000175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 Building ZINC001642000175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642000175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 206) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001642000175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642000175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001642000175 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 207) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1) `ZINC001642000175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642000175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001642000175 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=NS(=O)(=O)c2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 8, 14, 11, 11, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 9, 9, 9, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642000175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642000175 Building ZINC001642206006 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206006 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/208 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206006 none COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 31, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 12, 12, 11, 11, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/209 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206006 none COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 42, 14, 3, 3, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 42, 42, 42, 18, 18, 14, 14, 3, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206006 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 Building ZINC001642206006 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206006 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 208) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206006 none COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 31, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 12, 12, 11, 11, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 209) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206006 none COC(=O)CCNC(=O)[C@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 42, 14, 3, 3, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 42, 42, 42, 18, 18, 14, 14, 3, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206006 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206006 Building ZINC001642206007 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206007 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/210 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206007 none COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 31, 8, 4, 4, 2, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 31, 31, 31, 8, 8, 8, 8, 4, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/211 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206007 none COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 45, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 45, 45, 45, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206007 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 Building ZINC001642206007 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206007 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 210) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206007 none COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 31, 8, 4, 4, 2, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 31, 31, 31, 8, 8, 8, 8, 4, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 211) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206007 none COC(=O)CCNC(=O)[C@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 45, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 45, 45, 45, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206007 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206007 Building ZINC001642206008 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206008 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/212 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206008 none COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 45, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 45, 45, 45, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/213 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206008 none COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 30, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 30, 30, 30, 9, 9, 8, 8, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206008 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 Building ZINC001642206008 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206008 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 212) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206008 none COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 45, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 45, 45, 45, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 213) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206008 none COC(=O)CCNC(=O)[C@@H]1CS[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 30, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 30, 30, 30, 9, 9, 8, 8, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206008 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206008 Building ZINC001642206009 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206009 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/214 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206009 none COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 50, 16, 6, 6, 2, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 50, 50, 50, 21, 21, 16, 16, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/215 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206009 none COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 29, 29, 29, 11, 11, 10, 10, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206009 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 Building ZINC001642206009 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642206009 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 214) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642206009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206009 none COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 50, 16, 6, 6, 2, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 50, 50, 50, 21, 21, 16, 16, 6, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 215) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001642206009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642206009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001642206009 none COC(=O)CCNC(=O)[C@@H]1CS[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 5, 14, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 29, 29, 29, 11, 11, 10, 10, 3, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [45, 43, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 44, 19, 20, 46, 18, 42, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/194367/xbs-8058088.45/working/building/ZINC001642206009 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001642206009 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001642206009 Building ZINC001643391767 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643391767 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/216 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001643391767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643391767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001643391767 none COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 1, 11, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 19, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 36, 36, 36, 23, 23, 19, 19, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [40, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/217 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001643391767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643391767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001643391767 none COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 1, 11, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 36, 19, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 36, 36, 36, 22, 22, 19, 19, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [40, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001643391767 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 Building ZINC001643391767 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643391767 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 216) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001643391767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643391767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001643391767 none COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 1, 11, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 19, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 36, 36, 36, 23, 23, 19, 19, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [40, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 217) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001643391767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643391767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001643391767 none COC(=O)CCSc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 12, 1, 11, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 36, 19, 8, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 36, 36, 36, 22, 22, 19, 19, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [40, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001643391767 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643391767 Building ZINC001643635773 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643635773 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/218 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1) `ZINC001643635773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643635773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001643635773 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 5, 5, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 4, 4, 1, 5, 5, 9, 9, 5, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/219 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1) `ZINC001643635773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643635773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001643635773 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 22, 22, 24, 24, 24, 24, 4, 2, 2, 2, 2, 5, 5, 2, 4, 4, 7, 7, 4, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001643635773 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 Building ZINC001643635773 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643635773 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 218) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1) `ZINC001643635773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643635773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001643635773 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 9, 9, 5, 9, 9, 5, 5, 5, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 4, 4, 1, 5, 5, 9, 9, 5, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 219) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1) `ZINC001643635773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643635773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001643635773 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)[C@H](C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 22, 22, 24, 24, 24, 24, 4, 2, 2, 2, 2, 5, 5, 2, 4, 4, 7, 7, 4, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001643635773 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001643635773 Building ZINC001645170372 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001645170372 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/220 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001645170372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170372 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 20, 20, 20, 20, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/221 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001645170372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170372 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 17, 17, 17, 17, 1, 1, 1, 1, 4, 4, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001645170372 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 Building ZINC001645170372 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001645170372 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 220) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001645170372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170372 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 20, 20, 20, 20, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 221) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001645170372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170372 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 17, 17, 17, 17, 1, 1, 1, 1, 4, 4, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001645170372 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170372 Building ZINC001645170373 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001645170373 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/222 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001645170373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170373 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/223 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001645170373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170373 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 24, 25, 25, 25, 2, 2, 2, 2, 8, 8, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001645170373 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 Building ZINC001645170373 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001645170373 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 222) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001645170373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170373 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 223) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C) `ZINC001645170373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001645170373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001645170373 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CCCCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 24, 25, 25, 25, 2, 2, 2, 2, 8, 8, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001645170373 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645170373 Building ZINC001645572350 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001645572350 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/224 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1) `ZINC001645572350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001645572350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001645572350 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 22, 22, 22, 22, 22, 22, 22, 20, 20, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/225 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1) `ZINC001645572350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001645572350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001645572350 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 25, 25, 25, 25, 25, 25, 25, 22, 22, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 25, 25, 25, 25, 25, 25, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001645572350 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 Building ZINC001645572350 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001645572350 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 224) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1) `ZINC001645572350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001645572350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001645572350 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 22, 22, 22, 22, 22, 22, 22, 20, 20, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 22, 22, 22, 22, 22, 22, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 225) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1) `ZINC001645572350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001645572350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001645572350 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC1(Cc2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 25, 25, 25, 25, 25, 25, 25, 22, 22, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 25, 25, 25, 25, 25, 25, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001645572350 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001645572350 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001645572350 Building ZINC001646407868 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001646407868 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/226 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001646407868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407868 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 15, 15, 15, 26, 26, 26, 26, 26, 26, 15, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/227 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001646407868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407868 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 18, 18, 18, 30, 30, 30, 30, 30, 30, 18, 5, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 5, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 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, 56]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001646407868 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 Building ZINC001646407868 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001646407868 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 226) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001646407868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407868 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 15, 15, 15, 26, 26, 26, 26, 26, 26, 15, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 15, 15, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 227) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001646407868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407868 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 18, 18, 18, 30, 30, 30, 30, 30, 30, 18, 5, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 5, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 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, 56]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001646407868 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407868 Building ZINC001646407869 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001646407869 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/228 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001646407869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407869 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29, 29, 15, 5, 4, 4, 4, 7, 7, 7, 4, 4, 2, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 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, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/229 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001646407869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407869 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 16, 16, 16, 27, 27, 27, 27, 27, 27, 16, 5, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 5, 5, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001646407869 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 Building ZINC001646407869 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001646407869 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 228) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001646407869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407869 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29, 29, 15, 5, 4, 4, 4, 7, 7, 7, 4, 4, 2, 5, 5, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 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, 56]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 229) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl) `ZINC001646407869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001646407869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001646407869 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(=O)N(C3CN(C(=O)OC(C)(C)C)C3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 16, 16, 16, 27, 27, 27, 27, 27, 27, 16, 5, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 5, 5, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001646407869 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001646407869 Building ZINC001649381305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001649381305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/230 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/231 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/232 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/232' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/233 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/233' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001649381305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 Building ZINC001649381305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001649381305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 230) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 231) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 232) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 233) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001649381305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 Building ZINC001649381305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001649381305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 230) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 231) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 232) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 233) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001649381305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 Building ZINC001649381305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001649381305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 230) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 231) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 232) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 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/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 233) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F) `ZINC001649381305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001649381305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001649381305 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 25, 25, 26, 26, 26, 26, 26, 13, 13] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001649381305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001649381305 Building ZINC001650910158 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001650910158 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/234 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1) `ZINC001650910158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001650910158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 5, 6, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 10, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 10, 10, 10, 10, 10, 10, 29, 10, 10, 5] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/235 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1) `ZINC001650910158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001650910158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 13, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 13, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13, 13, 13, 13, 13, 33, 13, 13, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001650910158 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 Building ZINC001650910158 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001650910158 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 234) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1) `ZINC001650910158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001650910158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 5, 6, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 10, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 10, 10, 10, 10, 10, 10, 29, 10, 10, 5] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 235) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1) `ZINC001650910158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001650910158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 13, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 13, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13, 13, 13, 13, 13, 13, 33, 13, 13, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001650910158 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910158 Building ZINC001650910159 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001650910159 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/236 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1) `ZINC001650910159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001650910159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910159 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 13, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 13, 13, 28, 13, 13, 5] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/237 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1) `ZINC001650910159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001650910159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910159 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 4, 4, 1, 1, 1, 1, 5, 6, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 10, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 10, 10, 10, 10, 10, 10, 30, 10, 10, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001650910159 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 Building ZINC001650910159 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001650910159 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 236) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1) `ZINC001650910159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001650910159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910159 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 7, 9, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 13, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 13, 13, 28, 13, 13, 5] 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 237) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1) `ZINC001650910159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001650910159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001650910159 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](n3nncc3I)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 8, 8, 1, 1, 18, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 4, 4, 1, 1, 1, 1, 5, 6, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 10, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 10, 10, 10, 10, 10, 10, 30, 10, 10, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001650910159 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001650910159 Building ZINC001651074282 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001651074282 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/238 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2) `ZINC001651074282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001651074282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001651074282 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 7, 7, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/239 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2) `ZINC001651074282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001651074282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001651074282 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 14, 14, 18, 19, 19, 19, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 6, 6, 2, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001651074282 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 Building ZINC001651074282 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001651074282 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 238) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2) `ZINC001651074282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001651074282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001651074282 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 7, 7, 2, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 239) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2) `ZINC001651074282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001651074282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001651074282 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)OC(C)(C)C)CCC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 14, 14, 18, 19, 19, 19, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 6, 6, 2, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001651074282 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001651074282 Building ZINC001653297681 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001653297681 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/240 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001653297681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297681 none CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 29, 47, 29, 29, 6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 6, 6, 29, 29] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/241 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001653297681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297681 none CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 26, 44, 26, 26, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 26, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 7, 7, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 26, 26] 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001653297681 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 Building ZINC001653297681 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001653297681 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 240) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001653297681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297681 none CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 29, 47, 29, 29, 6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 6, 6, 29, 29] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 241) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001653297681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297681 none CC(C)(C)OC(=O)N1CC(N2C[C@@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 26, 44, 26, 26, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 26, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 7, 7, 2, 5, 5, 5, 5, 5, 5, 5, 7, 7, 26, 26] 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001653297681 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297681 Building ZINC001653297683 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001653297683 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/242 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001653297683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297683 none CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 17, 31, 17, 17, 6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 6, 6, 17, 17] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/243 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001653297683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297683 none CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 36, 22, 22, 6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 22, 22, 22, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 6, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001653297683 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 Building ZINC001653297683 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001653297683 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 242) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001653297683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297683 none CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 17, 31, 17, 17, 6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 6, 6, 17, 17] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 243) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1) `ZINC001653297683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001653297683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001653297683 none CC(C)(C)OC(=O)N1CC(N2C[C@H](NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2=O)C1 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.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.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 36, 22, 22, 6, 6, 6, 4, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 22, 22, 22, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 6, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001653297683 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001653297683 Building ZINC001654035344 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001654035344 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/244 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001654035344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035344 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 1, 3, 3, 3, 10, 17, 17, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 4, 4, 4, 4, 12, 12, 4, 3, 10, 10, 51, 19, 19, 19, 19] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/245 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001654035344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035344 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 1, 4, 4, 4, 11, 19, 19, 22, 22, 22, 22, 22, 22, 19, 19, 19, 19, 3, 3, 3, 3, 10, 10, 3, 4, 11, 11, 57, 22, 22, 22, 22] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001654035344 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 Building ZINC001654035344 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001654035344 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 244) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001654035344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035344 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 1, 3, 3, 3, 10, 17, 17, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 4, 4, 4, 4, 12, 12, 4, 3, 10, 10, 51, 19, 19, 19, 19] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 245) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001654035344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035344 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 1, 4, 4, 4, 11, 19, 19, 22, 22, 22, 22, 22, 22, 19, 19, 19, 19, 3, 3, 3, 3, 10, 10, 3, 4, 11, 11, 57, 22, 22, 22, 22] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 171 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001654035344 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035344 Building ZINC001654035351 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001654035351 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/246 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001654035351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035351 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 7, 3, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 23, 23, 23, 23, 23, 23, 18, 19, 19, 19, 3, 3, 3, 3, 7, 7, 3, 2, 11, 11, 57, 23, 23, 23, 23] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 171 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/247 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001654035351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035351 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 1, 3, 3, 3, 10, 17, 17, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 4, 4, 4, 4, 12, 12, 4, 3, 10, 10, 51, 20, 20, 20, 20] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 167 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001654035351 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 Building ZINC001654035351 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001654035351 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 246) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001654035351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035351 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 7, 3, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 23, 23, 23, 23, 23, 23, 18, 19, 19, 19, 3, 3, 3, 3, 7, 7, 3, 2, 11, 11, 57, 23, 23, 23, 23] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 171 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 247) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F) `ZINC001654035351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001654035351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001654035351 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@](O)(c1ccccc1Cl)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 1, 3, 3, 3, 10, 17, 17, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 4, 4, 4, 4, 12, 12, 4, 3, 10, 10, 51, 20, 20, 20, 20] 150 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 167 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001654035351 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001654035351 Building ZINC000511712222 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511712222 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/248 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-]) `ZINC000511712222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511712222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511712222 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 35, 35, 13, 8, 13, 13, 8, 8, 8, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 8, 8, 35, 35, 35, 35, 35, 43, 43, 43, 35, 35, 8, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 35] 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: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/249 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-]) `ZINC000511712222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511712222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511712222 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 28, 28, 28, 28, 11, 6, 11, 11, 6, 6, 6, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 6, 6, 28, 28, 28, 28, 28, 37, 37, 37, 28, 28, 6, 6, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 6, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511712222 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 Building ZINC000511712222 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511712222 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 248) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-]) `ZINC000511712222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511712222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511712222 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 35, 35, 13, 8, 13, 13, 8, 8, 8, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 8, 8, 35, 35, 35, 35, 35, 43, 43, 43, 35, 35, 8, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 35] 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: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 249) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-]) `ZINC000511712222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511712222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511712222 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 28, 28, 28, 28, 11, 6, 11, 11, 6, 6, 6, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 6, 6, 28, 28, 28, 28, 28, 37, 37, 37, 28, 28, 6, 6, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 6, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511712222 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511712222 Building ZINC000512390895 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512390895 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/250 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1) `ZINC000512390895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512390895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000512390895 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 12, 12, 7, 7, 24, 24, 24, 12, 12, 12, 12, 12, 7, 7, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 7, 7, 7, 7, 12, 12, 24, 24, 24, 12, 7, 7, 7, 7, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/251 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1) `ZINC000512390895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512390895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000512390895 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 12, 12, 7, 7, 24, 24, 24, 12, 12, 12, 12, 12, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 7, 7, 7, 7, 12, 12, 24, 24, 24, 12, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000512390895 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 Building ZINC000512390895 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512390895 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 250) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1) `ZINC000512390895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512390895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000512390895 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 12, 12, 7, 7, 24, 24, 24, 12, 12, 12, 12, 12, 7, 7, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 7, 7, 7, 7, 12, 12, 24, 24, 24, 12, 7, 7, 7, 7, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 251) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1) `ZINC000512390895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512390895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000512390895 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(S(C)(=O)=O)cc3[N+](=O)[O-])CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 12, 12, 7, 7, 24, 24, 24, 12, 12, 12, 12, 12, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 7, 7, 7, 7, 12, 12, 24, 24, 24, 12, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000512390895 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512390895 Building ZINC000512904348 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512904348 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/252 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/252' -> `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)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])cc1) `ZINC000512904348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512904348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000512904348 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 14, 18, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 14, 14, 18, 18, 27, 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]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/253 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/253' -> `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)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])cc1) `ZINC000512904348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512904348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000512904348 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 17, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 2, 13, 13, 17, 17, 25, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000512904348 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 Building ZINC000512904348 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512904348 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 252) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])cc1) `ZINC000512904348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512904348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000512904348 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 14, 18, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 14, 14, 18, 18, 27, 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]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 253) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])cc1) `ZINC000512904348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512904348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000512904348 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1ccc([N+](=O)[O-])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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 17, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 2, 13, 13, 17, 17, 25, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 210 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000512904348 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512904348 Building ZINC000516841152 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516841152 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/254 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-]) `ZINC000516841152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516841152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000516841152 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 26, 26, 11, 7, 11, 11, 7, 7, 7, 3, 2, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 7, 7, 26, 26, 26, 26, 26, 32, 32, 32, 26, 26, 7, 7, 7, 7, 6, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 26] 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, 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/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/255 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-]) `ZINC000516841152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516841152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000516841152 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 13, 9, 13, 13, 9, 9, 9, 3, 1, 6, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 29, 29, 29, 27, 27, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 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, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516841152 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 Building ZINC000516841152 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516841152 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 254) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-]) `ZINC000516841152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516841152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000516841152 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 26, 26, 11, 7, 11, 11, 7, 7, 7, 3, 2, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 7, 7, 26, 26, 26, 26, 26, 32, 32, 32, 26, 26, 7, 7, 7, 7, 6, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 26] 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, 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/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 255) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-]) `ZINC000516841152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516841152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000516841152 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 13, 9, 13, 13, 9, 9, 9, 3, 1, 6, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 27, 27, 27, 27, 27, 29, 29, 29, 27, 27, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 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, 52, 53, 54, 55]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516841152 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516841152 Building ZINC000520681141 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520681141 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/256 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/256' -> `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)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1) `ZINC000520681141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520681141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520681141 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 13, 17, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 13, 13, 17, 47, 47, 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/257 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/257' -> `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)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1) `ZINC000520681141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520681141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520681141 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 13, 17, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 12, 12, 13, 13, 17, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000520681141 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 Building ZINC000520681141 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520681141 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 256) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1) `ZINC000520681141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520681141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520681141 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 13, 17, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 12, 12, 13, 13, 17, 47, 47, 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 257) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1) `ZINC000520681141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520681141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520681141 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 13, 17, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 12, 12, 13, 13, 17, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000520681141 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520681141 Building ZINC000604037648 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604037648 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/258 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000604037648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604037648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000604037648 none Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 18, 28, 28, 18, 18, 18, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/259 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000604037648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604037648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000604037648 none Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 25, 25, 15, 15, 15, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 25, 25, 25, 25, 25, 25, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000604037648 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 Building ZINC000604037648 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604037648 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 258) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000604037648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604037648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000604037648 none Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 18, 28, 28, 18, 18, 18, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 259) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000604037648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604037648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000604037648 none Cc1ccc([N+](=O)[O-])cc1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 25, 25, 15, 15, 15, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 25, 25, 25, 25, 25, 25, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000604037648 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604037648 Building ZINC000608902429 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608902429 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/260 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-]) `ZINC000608902429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608902429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000608902429 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 15, 22, 22, 15, 15, 15, 4, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/261 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-]) `ZINC000608902429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608902429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000608902429 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 23, 50, 50, 23, 14, 23, 23, 14, 14, 14, 4, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 14, 14, 14, 14, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000608902429 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 Building ZINC000608902429 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608902429 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 260) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-]) `ZINC000608902429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608902429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000608902429 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 15, 22, 22, 15, 15, 15, 4, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 261) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-]) `ZINC000608902429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608902429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000608902429 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 8, 11, 11, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 23, 50, 50, 23, 14, 23, 23, 14, 14, 14, 4, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 2, 2, 14, 14, 14, 14, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000608902429 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608902429 Building ZINC000919698976 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000919698976 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/262 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/262' -> `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([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/263 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/263' -> `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([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/264 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/264' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/265 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/265' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000919698976 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 Building ZINC000919698976 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000919698976 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 262) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 263) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 264) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 265) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000919698976 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 Building ZINC000919698976 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000919698976 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 262) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 263) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 264) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 265) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000919698976 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 Building ZINC000919698976 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000919698976 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 262) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 22, 22, 22, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 263) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 264) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 21, 21, 21, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 265) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1) `ZINC000919698976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000919698976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000919698976 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[N@@](c3ncccn3)CC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 24, 24, 24, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000919698976 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000919698976 Building ZINC001142286264 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286264 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/266 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142286264 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 20, 20, 20, 20, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 11, 11, 11, 11, 10, 40, 36, 40, 20, 20, 20, 20, 11, 11, 11] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/267 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142286264 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 21, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 42, 35, 42, 21, 21, 21, 21, 11, 11, 11] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286264 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 Building ZINC001142286264 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286264 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 266) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142286264 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 20, 20, 20, 20, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 11, 11, 11, 11, 10, 40, 36, 40, 20, 20, 20, 20, 11, 11, 11] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 267) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142286264 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 21, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 42, 35, 42, 21, 21, 21, 21, 11, 11, 11] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286264 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286264 Building ZINC001142688349 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688349 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/268 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142688349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001142688349 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 37, 47, 47, 47, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 6, 6, 12, 74, 47, 74, 37, 37, 37, 37, 6, 6, 2, 6, 6] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/269 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142688349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001142688349 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 37, 45, 45, 45, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 6, 6, 12, 74, 45, 74, 37, 37, 37, 37, 6, 6, 1, 6, 6] 200 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 268 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142688349 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 Building ZINC001142688349 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688349 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 268) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142688349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001142688349 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 37, 47, 47, 47, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 6, 6, 12, 74, 47, 74, 37, 37, 37, 37, 6, 6, 2, 6, 6] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 269) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142688349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001142688349 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 37, 37, 37, 37, 45, 45, 45, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 6, 6, 12, 74, 45, 74, 37, 37, 37, 37, 6, 6, 1, 6, 6] 200 rigid atoms, others: [1, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 268 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142688349 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688349 Building ZINC001181378450 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181378450 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/270 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181378450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181378450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001181378450 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 19, 29, 29, 29, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 10, 10, 10, 10, 10, 9, 38, 29, 38, 19, 19, 19, 19, 9, 9, 10, 10, 10, 10, 10] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/271 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181378450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181378450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001181378450 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 21, 34, 34, 34, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 10, 10, 9, 10, 10, 10, 42, 34, 42, 21, 21, 21, 21, 8, 8, 10, 10, 10, 10, 10] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181378450 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 Building ZINC001181378450 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181378450 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 270) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181378450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181378450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001181378450 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 19, 29, 29, 29, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 10, 10, 10, 10, 10, 9, 38, 29, 38, 19, 19, 19, 19, 9, 9, 10, 10, 10, 10, 10] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 271) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181378450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181378450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001181378450 none O=C(Nc1c(O)c(S(=O)(=O)O)c(O)c2c1C(=O)c1ccccc1C2=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 21, 34, 34, 34, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 10, 10, 9, 10, 10, 10, 42, 34, 42, 21, 21, 21, 21, 8, 8, 10, 10, 10, 10, 10] 200 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181378450 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378450 Building ZINC001183364754 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364754 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/272 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1) `ZINC001183364754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364754 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1 NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 12, 1, 11, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 12, 12, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 37, 37, 37, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 8, 42, 37, 42, 21, 21, 21, 21, 12, 12] 200 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]) total number of confs: 253 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/273 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1) `ZINC001183364754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364754 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1 NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 12, 1, 11, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 12, 12, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 37, 37, 37, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 8, 40, 37, 40, 20, 20, 20, 20, 12, 12] 200 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]) total number of confs: 253 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183364754 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 Building ZINC001183364754 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364754 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 272) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1) `ZINC001183364754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364754 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1 NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 12, 1, 11, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 12, 12, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 37, 37, 37, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 8, 42, 37, 42, 21, 21, 21, 21, 12, 12] 200 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]) total number of confs: 253 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 273) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1) `ZINC001183364754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364754 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(O)c(S(=O)(=O)O)c(O)c3c2C(=O)c2ccccc2C3=O)cc1 NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 12, 1, 11, 8, 1, 1, 12, 1, 14, 11, 11, 12, 1, 12, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 5, 5, 4, 7, 4, 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] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 12, 12, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 37, 37, 37, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 8, 40, 37, 40, 20, 20, 20, 20, 12, 12] 200 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]) total number of confs: 253 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183364754 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183364754 Building ZINC001542702565 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542702565 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/274 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/275 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 9, 44, 44, 44, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 44, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/276 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/276' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/277 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/277' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 16, 46, 46, 46, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 46, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001542702565 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 Building ZINC001542702565 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542702565 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 274) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 275) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 9, 44, 44, 44, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 44, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 276) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 277) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 16, 46, 46, 46, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 46, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001542702565 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 Building ZINC001542702565 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542702565 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 274) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 275) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 9, 44, 44, 44, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 44, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 276) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 277) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 16, 46, 46, 46, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 46, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001542702565 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 Building ZINC001542702565 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542702565 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 274) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 275) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 9, 44, 44, 44, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 44, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 276) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 8, 15, 46, 46, 46, 15, 15, 8, 8, 1, 1, 1, 1, 2, 2, 1, 2, 8, 8, 8, 8, 15, 15, 46, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 277) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1) `ZINC001542702565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542702565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001542702565 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccc(OC(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 16, 16, 9, 16, 46, 46, 46, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 1, 2, 9, 9, 9, 9, 16, 16, 46, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001542702565 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001542702565 Building ZINC001634752948 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752948 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/278 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/279 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/280 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/280' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/281 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/281' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752948 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 Building ZINC001634752948 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752948 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 278) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 279) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 280) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 281) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752948 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 Building ZINC001634752948 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752948 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 278) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 279) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 280) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 281) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752948 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 Building ZINC001634752948 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752948 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 278) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 279) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 280) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 10, 17, 17, 10, 10, 38, 42, 42, 17, 17, 10, 1, 1, 1, 1, 4, 4, 1, 2, 10, 10, 10, 10, 10, 10, 17, 17, 42, 17, 17, 10, 10] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 281) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752948 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 14, 14, 8, 8, 32, 34, 34, 14, 14, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 8, 8, 8, 8, 14, 14, 34, 14, 14, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752948 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752948 Building ZINC001634752949 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752949 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/282 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/283 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/284 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/284' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/285 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/285' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752949 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 Building ZINC001634752949 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752949 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 282) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 283) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 284) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 285) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752949 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 Building ZINC001634752949 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752949 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 282) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 283) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 284) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 285) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752949 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 Building ZINC001634752949 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634752949 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 282) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 283) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 284) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 8, 8, 31, 33, 33, 12, 12, 8, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 8, 8, 12, 12, 33, 12, 12, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 285) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1) `ZINC001634752949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634752949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001634752949 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2ccc(OC(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 14, 14, 9, 9, 37, 40, 40, 14, 14, 9, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 9, 9, 9, 9, 14, 14, 40, 14, 14, 9, 9] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC001634752949 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634752949 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634752949 Building ZINC000728608627 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000728608627 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/286 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000728608627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000728608627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000728608627 none C#CCNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 7, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 7, 6, 6, 3, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/287 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000728608627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000728608627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000728608627 none C#CCNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 10, 5, 4, 4, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000728608627 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 Building ZINC000728608627 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000728608627 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 286) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C#CCNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000728608627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000728608627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000728608627 none C#CCNC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 7, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 7, 6, 6, 3, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 287) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C#CCNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000728608627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000728608627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000728608627 none C#CCNC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 4, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 10, 5, 4, 4, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000728608627 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000728608627 Building ZINC001142287723 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287723 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/288 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/289 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/290 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/290' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/291 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/291' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142287723 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 Building ZINC001142287723 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287723 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 288) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 289) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 290) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 291) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142287723 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 Building ZINC001142287723 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287723 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 288) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 289) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 290) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 291) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142287723 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 Building ZINC001142287723 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287723 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 288) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 289) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 19, 19, 28, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 17, 17, 28, 28, 40, 40, 40] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 290) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 291) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142287723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142287723 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccco3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'O.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 23, 23, 33, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 21, 4, 8, 8, 8, 21, 21, 33, 33, 42, 42, 42] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142287723 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287723 Building ZINC001142687040 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687040 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/292 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142687040 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 36, 36, 38, 38, 38, 38, 3, 5, 5, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 9, 9, 9, 9, 9, 9, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 12, 12, 12, 12, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/293 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142687040 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 11, 26, 26, 26, 26, 26, 26, 3, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 3, 1, 1, 1, 4, 4, 1, 4, 4, 5, 5, 5, 5, 5, 5, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 10, 10, 10, 10, 4, 4, 1, 4, 4] 35 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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: 114 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142687040 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 Building ZINC001142687040 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687040 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 292) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142687040 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 36, 36, 38, 38, 38, 38, 3, 5, 5, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 9, 9, 9, 9, 9, 9, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 12, 12, 12, 12, 2, 2, 1, 2, 2] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 293) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142687040 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 11, 26, 26, 26, 26, 26, 26, 3, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 3, 1, 1, 1, 4, 4, 1, 4, 4, 5, 5, 5, 5, 5, 5, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 10, 10, 10, 10, 4, 4, 1, 4, 4] 35 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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: 114 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142687040 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142687040 Building ZINC001142691870 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691870 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/294 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/295 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/296 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/296' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/297 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/297' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142691870 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 Building ZINC001142691870 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691870 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 294) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 295) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 296) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 297) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142691870 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 Building ZINC001142691870 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691870 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 294) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 295) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 296) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 297) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142691870 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 Building ZINC001142691870 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691870 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 294) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 295) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 21, 24, 24, 38, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4, 2, 2, 1, 2, 2, 21, 21, 38, 38, 50, 50, 50] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 296) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 297) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O) `ZINC001142691870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142691870 none Cn1c(=O)cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccccc3)C2)n(Cc2cc(F)ccc2C#N)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 17, 20, 20, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 3, 2, 2, 1, 2, 2, 17, 17, 39, 39, 50, 50, 50] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142691870 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142691870 Building ZINC001142697809 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142697809 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/298 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 37, 37, 20, 20, 41, 41, 41, 37, 37, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 37, 41, 41, 37, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 222 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/299 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 34, 34, 20, 29, 40, 40, 40, 34, 34, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 34, 40, 40, 34, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/300 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/300' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 35, 35, 31, 31, 41, 41, 41, 35, 35, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 35, 41, 41, 35, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/301 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/301' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 19, 19, 19, 19, 19, 37, 37, 19, 30, 42, 42, 42, 37, 37, 19, 19, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 19, 19, 19, 19, 37, 42, 42, 37, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 214 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142697809 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 Building ZINC001142697809 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142697809 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 298) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 37, 37, 20, 20, 41, 41, 41, 37, 37, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 37, 41, 41, 37, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 222 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 299) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 34, 34, 20, 29, 40, 40, 40, 34, 34, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 34, 40, 40, 34, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 300) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 35, 35, 31, 31, 41, 41, 41, 35, 35, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 35, 41, 41, 35, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 301) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 19, 19, 19, 19, 19, 37, 37, 19, 30, 42, 42, 42, 37, 37, 19, 19, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 19, 19, 19, 19, 37, 42, 42, 37, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 214 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142697809 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 Building ZINC001142697809 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142697809 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 298) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 37, 37, 20, 20, 41, 41, 41, 37, 37, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 37, 41, 41, 37, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 222 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 299) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 34, 34, 20, 29, 40, 40, 40, 34, 34, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 34, 40, 40, 34, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 300) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 35, 35, 31, 31, 41, 41, 41, 35, 35, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 35, 41, 41, 35, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 301) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 19, 19, 19, 19, 19, 37, 37, 19, 30, 42, 42, 42, 37, 37, 19, 19, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 19, 19, 19, 19, 37, 42, 42, 37, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 214 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142697809 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 Building ZINC001142697809 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142697809 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 298) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 37, 37, 20, 20, 41, 41, 41, 37, 37, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 37, 41, 41, 37, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 222 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 299) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 34, 34, 20, 29, 40, 40, 40, 34, 34, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 34, 40, 40, 34, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 194 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 300) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 20, 20, 20, 20, 20, 35, 35, 31, 31, 41, 41, 41, 35, 35, 20, 20, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 20, 20, 20, 20, 35, 41, 41, 35, 20, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 301) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21) `ZINC001142697809.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142697809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 4 26 3 30 to be deleted 31 to be deleted 32 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142697809 none Cn1cc(CN(C[C@H]2CC[N@@](c3ncc(C(=O)NO)cn3)CC2)C(=O)[C@@](C)([O-])[SiH3])c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 5, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 12, 1, 8, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 4, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 2, 3, 9, 19, 19, 19, 19, 19, 37, 37, 19, 30, 42, 42, 42, 37, 37, 19, 19, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 19, 19, 19, 19, 37, 42, 42, 37, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [56, 55, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 58, 59, 60, 61]) total number of confs: 214 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142697809 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142697809 Building ZINC001144037164 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144037164 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/302 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001144037164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144037164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001144037164 none CCC[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 5, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 5, 5, 12, 19, 19, 19, 19, 19, 19] 22 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 75 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/303 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001144037164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144037164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001144037164 none CCC[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5] 7 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144037164 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 Building ZINC001144037164 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144037164 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 302) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001144037164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144037164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001144037164 none CCC[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 5, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 5, 5, 12, 19, 19, 19, 19, 19, 19] 22 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 75 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 303) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001144037164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144037164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001144037164 none CCC[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5] 7 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144037164 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037164 Building ZINC001144042803 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144042803 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/304 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/305 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/306 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/306' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/307 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/307' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144042803 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 Building ZINC001144042803 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144042803 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 304) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 305) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 306) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 307) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144042803 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 Building ZINC001144042803 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144042803 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 304) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 305) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 306) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 307) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144042803 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 Building ZINC001144042803 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144042803 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 304) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 305) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 306) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 39, 46, 46, 46, 46, 46, 46, 46, 46, 11, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 39, 39, 46, 46, 46, 11, 11] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 307) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001144042803.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144042803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001144042803 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 2, 2, 3, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 40, 47, 47, 47, 47, 47, 47, 47, 47, 12, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 40, 40, 47, 47, 47, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58]) total number of confs: 169 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144042803 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144042803 Building ZINC001181376286 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376286 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/308 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181376286 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 15, 24, 32, 32, 33, 33, 33, 33, 4, 4, 4, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 24, 24, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/309 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181376286 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 19, 29, 29, 30, 30, 30, 30, 3, 4, 4, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 136 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181376286 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 Building ZINC001181376286 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376286 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 308) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181376286 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 15, 24, 32, 32, 33, 33, 33, 33, 4, 4, 4, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 24, 24, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 309) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181376286 none CC(C)(CC(=O)N1CCCC1)N(CC(=O)N1C[C@@H](F)C[C@H]1C#N)C(=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 1, 11, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 19, 29, 29, 30, 30, 30, 30, 3, 4, 4, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 136 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181376286 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181376286 Building ZINC001183097140 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097140 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/310 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097140 none N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 16, 16, 13, 3, 16, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/311 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097140 none N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 10, 3, 12, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 20, 20, 20, 20, 20, 12, 12, 12, 12, 18, 18] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097140 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 Building ZINC001183097140 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097140 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 310) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097140 none N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 16, 16, 13, 3, 16, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20, 20, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 311) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097140 none N#Cc1ccc(N2C[C@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 10, 3, 12, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 20, 20, 20, 20, 20, 12, 12, 12, 12, 18, 18] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097140 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097140 Building ZINC001183097143 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097143 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/312 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097143 none N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 11, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 18, 18, 18, 18, 18, 11, 11, 11, 11, 21, 21] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/313 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097143 none N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 10, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 18, 18, 18, 18, 18, 10, 10, 10, 10, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097143 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 Building ZINC001183097143 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097143 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 312) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097143 none N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 11, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 18, 18, 18, 18, 18, 11, 11, 11, 11, 21, 21] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 313) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1) `ZINC001183097143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097143 none N#Cc1ccc(N2C[C@@]3(COCCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)OCC2=O)cc1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.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: [8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 11, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 10, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 18, 18, 18, 18, 18, 10, 10, 10, 10, 15, 15] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097143 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097143 Building ZINC001183366012 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183366012 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/314 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1) `ZINC001183366012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183366012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183366012 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2] 8 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/315 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1) `ZINC001183366012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183366012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183366012 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2] 3 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 17 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183366012 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 Building ZINC001183366012 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183366012 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 314) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1) `ZINC001183366012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183366012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183366012 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2] 8 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 315) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1) `ZINC001183366012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183366012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183366012 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(=O)N2C[C@@H](F)C[C@H]2C#N)C(C)(C)CC(=O)N2CCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 15, 5, 5, 7, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2] 3 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 17 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183366012 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183366012 Building ZINC001184247890 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247890 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/316 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247890 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [21, 14, 14, 14, 7, 1, 1, 1, 2, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 14, 14, 14, 14, 21, 21, 21, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 12, 12, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/317 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247890 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [17, 10, 10, 10, 6, 1, 1, 1, 2, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 12, 12, 12, 14, 14, 11, 11, 11, 11, 11, 10, 10, 10, 10, 17, 17, 17, 10, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 11, 11, 11, 11, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184247890 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 Building ZINC001184247890 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247890 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 316) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247890 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [21, 14, 14, 14, 7, 1, 1, 1, 2, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 14, 14, 14, 14, 21, 21, 21, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 12, 12, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 317) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247890 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [17, 10, 10, 10, 6, 1, 1, 1, 2, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 12, 12, 12, 14, 14, 11, 11, 11, 11, 11, 10, 10, 10, 10, 17, 17, 17, 10, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 11, 11, 11, 11, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184247890 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247890 Building ZINC001184247898 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247898 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/318 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247898 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [20, 11, 11, 11, 6, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 12, 12, 12, 16, 16, 12, 12, 12, 12, 12, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 12, 12, 12, 12, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/319 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247898 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [26, 15, 15, 15, 8, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 10, 10, 10, 14, 14, 10, 10, 10, 10, 10, 15, 15, 15, 15, 26, 26, 26, 15, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 10, 10, 10, 10, 15, 15, 30] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 129 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184247898 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 Building ZINC001184247898 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247898 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 318) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247898 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [20, 11, 11, 11, 6, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 12, 12, 12, 16, 16, 12, 12, 12, 12, 12, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 12, 12, 12, 12, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 319) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O) `ZINC001184247898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184247898 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCOC[C@@]3(CN(c4ccc(C#N)cc4)C(=O)CO3)C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 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] 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: [26, 15, 15, 15, 8, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 10, 10, 10, 14, 14, 10, 10, 10, 10, 10, 15, 15, 15, 15, 26, 26, 26, 15, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 10, 10, 10, 10, 15, 15, 30] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 129 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184247898 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184247898 Building ZINC001184248988 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248988 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/320 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O) `ZINC001184248988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248988 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 15, 15, 14, 15, 21, 21, 21, 15, 15, 8, 8, 8, 8, 18, 18, 18, 8, 4, 4, 5, 11, 15, 15, 21, 21, 21, 15, 15, 8, 8, 16] 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, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/321 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O) `ZINC001184248988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248988 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 21, 21, 21, 15, 15, 8, 8, 8, 8, 18, 18, 18, 8, 4, 4, 5, 11, 15, 15, 21, 21, 21, 15, 15, 8, 8, 16] 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, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184248988 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 Building ZINC001184248988 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248988 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 320) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O) `ZINC001184248988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248988 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 15, 15, 14, 15, 21, 21, 21, 15, 15, 8, 8, 8, 8, 18, 18, 18, 8, 4, 4, 5, 11, 15, 15, 21, 21, 21, 15, 15, 8, 8, 16] 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, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 321) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O) `ZINC001184248988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248988 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C#N)cnn2c2ccc(S(C)(=O)=O)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 21, 21, 21, 15, 15, 8, 8, 8, 8, 18, 18, 18, 8, 4, 4, 5, 11, 15, 15, 21, 21, 21, 15, 15, 8, 8, 16] 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, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184248988 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184248988 Building ZINC001184249049 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249049 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/322 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/323 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/324 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/324' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/325 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/325' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249049 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 Building ZINC001184249049 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249049 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 322) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 323) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 324) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 325) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249049 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 Building ZINC001184249049 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249049 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 322) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 323) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 324) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 325) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249049 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 Building ZINC001184249049 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249049 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 322) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 323) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 324) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 11, 11, 6, 1, 1, 1, 2, 6, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 8, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 8, 11, 11, 22] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 325) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249049.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249049 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 14, 14, 7, 1, 1, 1, 2, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 14, 14, 14, 14, 20, 20, 20, 14, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 12, 12, 14, 14, 28] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249049 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249049 Building ZINC001184249050 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249050 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/326 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/327 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/328 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/328' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/329 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/329' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249050 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 Building ZINC001184249050 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249050 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 326) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 327) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 328) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 329) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249050 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 Building ZINC001184249050 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249050 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 326) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 327) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 328) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 329) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249050 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 Building ZINC001184249050 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249050 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 326) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 327) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 328) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 7, 7, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 329) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O) `ZINC001184249050.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184249050 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(c2cccc(C#N)n2)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 10, 10, 5, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 10, 10, 10, 10, 15, 15, 15, 10, 5, 5, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 22, 8, 8, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249050 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249050 Building ZINC001184318834 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318834 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/330 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318834 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 5, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 5, 5, 9, 14, 14, 14, 14, 14, 14] 18 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 58 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/331 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318834 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 5, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 17, 31, 31, 31, 31, 31, 31] 45 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184318834 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 Building ZINC001184318834 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318834 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 330) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318834 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 3, 3, 3, 5, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 5, 5, 9, 14, 14, 14, 14, 14, 14] 18 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 58 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 331) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318834 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 5, 17, 17, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 17, 31, 31, 31, 31, 31, 31] 45 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 94 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184318834 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318834 Building ZINC001184318835 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318835 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/332 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318835 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 3, 5, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 5, 5, 13, 22, 22, 22, 22, 22, 22] 33 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 90 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/333 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318835 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 43, 44, 45, 8, 21, 9, 7, 6, 10] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184318835 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 Building ZINC001184318835 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318835 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 332) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318835 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 2, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 3, 5, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 5, 5, 13, 22, 22, 22, 22, 22, 22] 33 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 90 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 333) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1) `ZINC001184318835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184318835 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CC(=O)N1CCC[C@H]1C#N)C(C)(C)CNC(=O)c1cnc2cc(C)nn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 7, 7, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 43, 44, 45, 8, 21, 9, 7, 6, 10] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184318835 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184318835 Building ZINC001184323175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/334 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/335 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/336 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/336' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/337 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/337' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 Building ZINC001184323175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 334) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 335) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 336) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 337) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 Building ZINC001184323175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 334) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 335) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 336) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 337) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 Building ZINC001184323175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 334) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 335) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 336) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 49, 49, 49, 49, 49, 49, 49, 49, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 49, 49, 49, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 337) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323175.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323175 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 41, 50, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 41, 41, 50, 50, 50, 19, 19] 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, 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/194367/xbs-8058088.45/working/building/ZINC001184323175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323175 Building ZINC001184323176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/338 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/339 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/340 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/340' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/341 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/341' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 Building ZINC001184323176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 338) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 339) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 340) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 341) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 Building ZINC001184323176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 338) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 339) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 340) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 341) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 Building ZINC001184323176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184323176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 338) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 339) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 340) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 40, 50, 50, 50, 50, 50, 50, 50, 50, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 23, 23, 23, 23, 40, 40, 50, 50, 50, 16, 16] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 341) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184323176.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184323176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184323176 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 5, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 40, 50, 50, 50, 50, 50, 50, 50, 50, 17, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 40, 40, 50, 50, 50, 17, 17] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184323176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184323176 Building ZINC001184330977 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330977 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/342 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@@]([O-])([SiH3])CC(C)C)cn2n1) `ZINC001184330977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330977 none Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@@]([O-])([SiH3])CC(C)C)cn2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 12, 12, 12, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 12, 6, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 18 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 68]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/343 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@]([O-])([SiH3])CC(C)C)cn2n1) `ZINC001184330977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330977 none Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@]([O-])([SiH3])CC(C)C)cn2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 11, 11, 11, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 11, 7, 7, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 16 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 68]) total number of confs: 52 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184330977 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 Building ZINC001184330977 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330977 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 342) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@@]([O-])([SiH3])CC(C)C)cn2n1) `ZINC001184330977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330977 none Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@@]([O-])([SiH3])CC(C)C)cn2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 12, 12, 12, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 12, 6, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 18 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 68]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 343) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@]([O-])([SiH3])CC(C)C)cn2n1) `ZINC001184330977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330977 none Cc1cc2ncc(C(=O)NCC(C)(C)N(CC(=O)N3CCC[C@H]3C#N)C(=O)[C@]([O-])([SiH3])CC(C)C)cn2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 11, 11, 11, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 11, 7, 7, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 16 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 68]) total number of confs: 52 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184330977 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184330977 Building ZINC001184333019 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184333019 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/344 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/345 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/346 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/346' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/347 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/347' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184333019 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 Building ZINC001184333019 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184333019 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 344) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 345) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 346) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 347) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184333019 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 Building ZINC001184333019 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184333019 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 344) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 345) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 346) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 347) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184333019 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 Building ZINC001184333019 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184333019 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 344) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 345) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 346) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 42, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 42, 42, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 6, 5] set([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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 347) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1) `ZINC001184333019.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184333019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001184333019 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(=O)n(C)c(=O)n2Cc2cc(F)ccc2C#N)C1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 44, 44, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 8, 3, 7, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184333019 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184333019 Building ZINC001184487425 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487425 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/348 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487425 none NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 8, 3, 2, 3, 5, 8, 8, 8, 17, 23, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 9, 9, 8, 8, 5, 5, 24, 23, 23, 3, 3, 3, 3] 150 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]) total number of confs: 150 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/349 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487425 none NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 11, 3, 2, 3, 3, 5, 5, 5, 10, 14, 14, 14, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 15, 15, 11, 11, 3, 3, 15, 14, 14, 4, 4, 4, 4] 129 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]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184487425 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 Building ZINC001184487425 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487425 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 348) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487425 none NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 8, 3, 2, 3, 5, 8, 8, 8, 17, 23, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 9, 9, 8, 8, 5, 5, 24, 23, 23, 3, 3, 3, 3] 150 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]) total number of confs: 150 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 349) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487425 none NCCCN(C[C@@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [24, 15, 11, 3, 2, 3, 3, 5, 5, 5, 10, 14, 14, 14, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 15, 15, 11, 11, 3, 3, 15, 14, 14, 4, 4, 4, 4] 129 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]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184487425 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487425 Building ZINC001184487427 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487427 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/350 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487427 none NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 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: [28, 18, 14, 3, 2, 3, 4, 6, 6, 6, 11, 13, 13, 13, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 18, 18, 14, 14, 4, 4, 18, 13, 13, 4, 4, 4, 4] 150 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]) total number of confs: 190 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/351 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487427 none NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 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: [15, 11, 10, 4, 3, 4, 5, 7, 7, 7, 20, 27, 27, 27, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 11, 11, 10, 10, 5, 5, 21, 27, 27, 4, 4, 4, 4] 150 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]) total number of confs: 162 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184487427 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 Building ZINC001184487427 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487427 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 350) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487427 none NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 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: [28, 18, 14, 3, 2, 3, 4, 6, 6, 6, 11, 13, 13, 13, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 18, 18, 14, 14, 4, 4, 18, 13, 13, 4, 4, 4, 4] 150 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]) total number of confs: 190 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 351) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184487427 none NCCCN(C[C@H](S)OP(=O)(O)O)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [10, 5, 5, 5, 8, 5, 5, 7, 14, 12, 13, 11, 12, 12, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 4, 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] 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: [15, 11, 10, 4, 3, 4, 5, 7, 7, 7, 20, 27, 27, 27, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 11, 11, 10, 10, 5, 5, 21, 27, 27, 4, 4, 4, 4] 150 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]) total number of confs: 162 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184487427 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184487427 Building ZINC001184488324 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488324 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/352 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488324 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 13, 16, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 20, 20, 25, 25, 20, 20, 20, 20, 20, 5, 5, 8, 8, 8, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 25, 25, 20, 20, 20, 20, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/353 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488324 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 2, 8, 11, 16, 16, 16, 16, 16, 16, 16, 16, 26, 26, 16, 18, 21, 26, 26, 16, 16, 16, 16, 16, 5, 5, 8, 8, 8, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 26, 26, 26, 26, 16, 16, 16, 16, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184488324 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 Building ZINC001184488324 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488324 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 352) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488324 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 3, 13, 16, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 20, 20, 25, 25, 20, 20, 20, 20, 20, 5, 5, 8, 8, 8, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 25, 25, 20, 20, 20, 20, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 353) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488324 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 2, 8, 11, 16, 16, 16, 16, 16, 16, 16, 16, 26, 26, 16, 18, 21, 26, 26, 16, 16, 16, 16, 16, 5, 5, 8, 8, 8, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 26, 26, 26, 26, 16, 16, 16, 16, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184488324 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488324 Building ZINC001184488325 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488325 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/354 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488325 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 2, 11, 12, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 17, 17, 17, 17, 17, 5, 5, 8, 8, 8, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 17, 17, 17, 17, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/355 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488325 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 11, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 15, 5, 5, 7, 7, 7, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 15, 15, 15, 15, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184488325 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 Building ZINC001184488325 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488325 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 354) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488325 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 2, 11, 12, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 17, 17, 17, 17, 17, 5, 5, 8, 8, 8, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 17, 17, 17, 17, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 355) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1) `ZINC001184488325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184488325 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccc(C#N)cc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 11, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 15, 5, 5, 7, 7, 7, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 15, 15, 15, 15, 5] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184488325 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184488325 Building ZINC001449276115 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449276115 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/356 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449276115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276115 none CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 15, 29, 15, 15, 15, 15, 15, 15, 12, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 12, 12, 8, 12, 12, 12, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 9, 9, 3, 8, 8, 12, 12, 12, 12, 15, 15, 15, 15, 33, 33, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/357 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449276115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276115 none CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 28, 19, 28, 19, 19, 19, 19, 19, 19, 14, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 10, 10, 3, 6, 6, 9, 9, 9, 9, 19, 19, 19, 19, 34, 34, 34, 34] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001449276115 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 Building ZINC001449276115 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449276115 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 356) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449276115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276115 none CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 15, 29, 15, 15, 15, 15, 15, 15, 12, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 12, 12, 8, 12, 12, 12, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 9, 9, 3, 8, 8, 12, 12, 12, 12, 15, 15, 15, 15, 33, 33, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 357) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449276115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276115 none CN1CCN(C(=O)c2cnn3c2C[C@@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 28, 19, 28, 19, 19, 19, 19, 19, 19, 14, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 10, 10, 3, 6, 6, 9, 9, 9, 9, 19, 19, 19, 19, 34, 34, 34, 34] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001449276115 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276115 Building ZINC001449276116 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449276116 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/358 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449276116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276116 none CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 26, 14, 26, 14, 14, 14, 14, 14, 14, 11, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 8, 8, 2, 6, 6, 9, 9, 9, 9, 14, 14, 14, 14, 30, 30, 30, 30] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/359 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449276116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276116 none CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 26, 14, 26, 14, 14, 14, 14, 14, 14, 11, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 5, 5, 7, 7, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 9, 9, 3, 5, 5, 7, 7, 7, 7, 14, 14, 14, 14, 30, 30, 30, 30] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001449276116 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 Building ZINC001449276116 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449276116 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 358) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449276116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276116 none CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 26, 14, 26, 14, 14, 14, 14, 14, 14, 11, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 8, 8, 2, 6, 6, 9, 9, 9, 9, 14, 14, 14, 14, 30, 30, 30, 30] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 359) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1) `ZINC001449276116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449276116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001449276116 none CN1CCN(C(=O)c2cnn3c2C[C@H](CNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 26, 14, 26, 14, 14, 14, 14, 14, 14, 11, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 5, 5, 7, 7, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 9, 9, 3, 5, 5, 7, 7, 7, 7, 14, 14, 14, 14, 30, 30, 30, 30] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001449276116 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001449276116 Building ZINC001558653732 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558653732 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/360 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001558653732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558653732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001558653732 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 11, 2, 11, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 12, 5, 5, 8, 8, 8, 8, 12, 12, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/361 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001558653732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558653732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001558653732 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 16, 10, 10, 10, 7, 2, 7, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 6, 6, 9, 9, 9, 9, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001558653732 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 Building ZINC001558653732 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558653732 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 360) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001558653732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558653732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001558653732 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 11, 2, 11, 1, 1, 1, 5, 5, 8, 8, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12, 12, 5, 5, 8, 8, 8, 8, 12, 12, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 361) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001558653732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558653732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001558653732 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)[C@@H]2CS(=O)(=O)C[C@@H]21 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 16, 10, 10, 10, 7, 2, 7, 1, 1, 1, 6, 6, 9, 9, 6, 6, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 6, 6, 9, 9, 9, 9, 10, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001558653732 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001558653732 Building ZINC001634269838 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634269838 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/362 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634269838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269838 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 42, 43, 43, 30, 13, 30, 13, 13, 13, 13, 13, 13, 11, 13, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 11, 11, 6, 6, 11, 11, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 13, 13, 13, 13, 11, 11, 11, 11, 4, 6, 6, 11, 11, 11, 11, 13, 13] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/363 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634269838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269838 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 19, 10, 19, 10, 10, 10, 10, 10, 10, 9, 10, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 12, 12, 8, 8, 12, 12, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 9, 9, 9, 9, 3, 8, 8, 12, 12, 12, 12, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634269838 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 Building ZINC001634269838 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634269838 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 362) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634269838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269838 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 42, 43, 43, 30, 13, 30, 13, 13, 13, 13, 13, 13, 11, 13, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 11, 11, 6, 6, 11, 11, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 13, 13, 13, 13, 11, 11, 11, 11, 4, 6, 6, 11, 11, 11, 11, 13, 13] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 363) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634269838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269838 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 19, 10, 19, 10, 10, 10, 10, 10, 10, 9, 10, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 12, 12, 8, 8, 12, 12, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 9, 9, 9, 9, 3, 8, 8, 12, 12, 12, 12, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634269838 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269838 Building ZINC001634269839 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634269839 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/364 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634269839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269839 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 17, 9, 17, 9, 9, 9, 9, 9, 9, 8, 9, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 9, 9, 7, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 8, 8, 8, 8, 3, 7, 7, 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, 52, 53, 54, 55, 56, 57]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/365 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634269839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269839 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 43, 44, 44, 32, 14, 32, 14, 14, 14, 14, 14, 14, 11, 14, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 11, 11, 7, 11, 11, 11, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14, 11, 11, 11, 11, 4, 6, 6, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634269839 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 Building ZINC001634269839 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634269839 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 364) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634269839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269839 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 17, 9, 17, 9, 9, 9, 9, 9, 9, 8, 9, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 9, 9, 7, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 8, 8, 8, 8, 3, 7, 7, 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, 52, 53, 54, 55, 56, 57]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 365) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1) `ZINC001634269839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634269839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001634269839 none CC(C)(C)OC(=O)N1CCS(=O)(=O)[C@H](CCNC(=O)[C@]([O-])([SiH3])/C=C/c2ccc(F)cc2)C1 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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 43, 44, 44, 32, 14, 32, 14, 14, 14, 14, 14, 14, 11, 14, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 11, 11, 7, 11, 11, 11, 14, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14, 11, 11, 11, 11, 4, 6, 6, 11, 11, 11, 11, 14, 14] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001634269839 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001634269839 Building ZINC001143972019 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972019 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/366 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12) `ZINC001143972019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001143972019 none CC[C@@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'Cl', 'C.3', 'S.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, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 16, 5, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 10, 10, 12, 30, 43, 43, 30, 38, 45, 43, 43, 4, 4, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 30, 30, 43, 43, 45, 45, 45, 43, 43, 9, 9, 4, 4] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/367 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12) `ZINC001143972019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001143972019 none CC[C@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'Cl', 'C.3', 'S.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, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 16, 5, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 9, 9, 11, 27, 43, 43, 27, 43, 45, 43, 43, 4, 4, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 27, 27, 43, 43, 45, 45, 45, 43, 43, 10, 10, 4, 4] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143972019 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 Building ZINC001143972019 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972019 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 366) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12) `ZINC001143972019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001143972019 none CC[C@@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'Cl', 'C.3', 'S.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, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 16, 5, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 10, 10, 12, 30, 43, 43, 30, 38, 45, 43, 43, 4, 4, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 30, 30, 43, 43, 45, 45, 45, 43, 43, 9, 9, 4, 4] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 367) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12) `ZINC001143972019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001143972019 none CC[C@]([O-])([SiH3])C(=O)N[C@@H]1C(=O)N2C(C(=O)OCc3ccc(OC)cc3)=C(CCl)CS[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'Cl', 'C.3', 'S.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, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 16, 5, 14, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 9, 9, 11, 27, 43, 43, 27, 43, 45, 43, 43, 4, 4, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 27, 27, 43, 43, 45, 45, 45, 43, 43, 10, 10, 4, 4] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143972019 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972019 Building ZINC001182671611 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182671611 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/368 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@@]([O-])([SiH3])C4CC4)C(=O)N23)cc1) `ZINC001182671611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182671611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001182671611 none COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@@]([O-])([SiH3])C4CC4)C(=O)N23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'Cl', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 5, 16, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 27, 44, 44, 27, 11, 9, 4, 9, 4, 4, 4, 10, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 27, 27, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 44, 44] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/369 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@]([O-])([SiH3])C4CC4)C(=O)N23)cc1) `ZINC001182671611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182671611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001182671611 none COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@]([O-])([SiH3])C4CC4)C(=O)N23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'Cl', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 5, 16, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 42, 26, 44, 44, 26, 11, 9, 4, 9, 4, 4, 4, 10, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 26, 26, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 44, 44] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182671611 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 Building ZINC001182671611 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182671611 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 368) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@@]([O-])([SiH3])C4CC4)C(=O)N23)cc1) `ZINC001182671611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182671611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001182671611 none COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@@]([O-])([SiH3])C4CC4)C(=O)N23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'Cl', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 5, 16, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 27, 44, 44, 27, 11, 9, 4, 9, 4, 4, 4, 10, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 27, 27, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 44, 44] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 369) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@]([O-])([SiH3])C4CC4)C(=O)N23)cc1) `ZINC001182671611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182671611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001182671611 none COc1ccc(COC(=O)C2=C(CCl)CS[C@@H]3[C@H](NC(=O)[C@]([O-])([SiH3])C4CC4)C(=O)N23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'Cl', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 1, 1, 5, 16, 5, 14, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 42, 26, 44, 44, 26, 11, 9, 4, 9, 4, 4, 4, 10, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 26, 26, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 44, 44] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 18, 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, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182671611 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182671611 Building ZINC001184249210 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249210 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/370 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O) `ZINC001184249210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249210 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 11, 8, 10, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 10, 10, 10, 5, 1, 1, 1, 1, 3, 3, 5, 12, 12, 16, 16, 16, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 18, 18, 18, 10, 5, 5, 5, 16, 16, 16, 12, 15, 15, 15, 15, 10, 10, 20] 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, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/371 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O) `ZINC001184249210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249210 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 11, 8, 10, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 11, 11, 11, 6, 1, 1, 1, 1, 3, 3, 6, 15, 15, 20, 20, 20, 15, 15, 15, 15, 17, 17, 15, 15, 17, 17, 11, 11, 11, 11, 21, 21, 21, 11, 6, 6, 6, 20, 20, 20, 15, 17, 17, 17, 17, 11, 11, 22] 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, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249210 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 Building ZINC001184249210 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249210 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 370) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O) `ZINC001184249210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249210 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 11, 8, 10, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 10, 10, 10, 5, 1, 1, 1, 1, 3, 3, 5, 12, 12, 16, 16, 16, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 18, 18, 18, 10, 5, 5, 5, 16, 16, 16, 12, 15, 15, 15, 15, 10, 10, 20] 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, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 371) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O) `ZINC001184249210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249210 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C(=O)NN)cnn2c2ccc(Br)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 11, 8, 10, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 11, 11, 11, 6, 1, 1, 1, 1, 3, 3, 6, 15, 15, 20, 20, 20, 15, 15, 15, 15, 17, 17, 15, 15, 17, 17, 11, 11, 11, 11, 21, 21, 21, 11, 6, 6, 6, 20, 20, 20, 15, 17, 17, 17, 17, 11, 11, 22] 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, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184249210 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184249210 Building ZINC001184484262 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484262 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/372 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484262 none N[C@@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [36, 29, 36, 20, 20, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 9, 9, 36, 38, 38, 36, 36, 29, 29, 13, 13, 2, 4, 4, 4, 4, 27, 114] 450 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: 310 number of broken/clashed sets: 167 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/373 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484262 none N[C@@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [27, 23, 27, 17, 17, 13, 9, 3, 9, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 11, 11, 27, 27, 27, 27, 27, 23, 23, 13, 13, 3, 4, 4, 4, 4, 33, 81] 450 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: 243 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184484262 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 Building ZINC001184484262 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484262 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 372) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N[C@@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484262 none N[C@@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [36, 29, 36, 20, 20, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 9, 9, 36, 38, 38, 36, 36, 29, 29, 13, 13, 2, 4, 4, 4, 4, 27, 114] 450 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: 310 number of broken/clashed sets: 167 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 373) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N[C@@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484262 none N[C@@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [27, 23, 27, 17, 17, 13, 9, 3, 9, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 11, 11, 27, 27, 27, 27, 27, 23, 23, 13, 13, 3, 4, 4, 4, 4, 33, 81] 450 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: 243 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184484262 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484262 Building ZINC001184484263 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484263 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/374 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484263 none N[C@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [36, 28, 36, 13, 12, 7, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 7, 7, 36, 39, 39, 36, 36, 28, 28, 7, 7, 2, 4, 4, 4, 4, 21, 117] 450 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: 309 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/375 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484263 none N[C@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 12, 12, 9, 7, 3, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 8, 8, 31, 31, 31, 31, 31, 31, 31, 9, 9, 3, 4, 4, 4, 4, 24, 93] 450 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: 251 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184484263 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 Building ZINC001184484263 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484263 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 374) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N[C@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484263 none N[C@H](CSSC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [36, 28, 36, 13, 12, 7, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 7, 7, 36, 39, 39, 36, 36, 28, 28, 7, 7, 2, 4, 4, 4, 4, 21, 117] 450 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: 309 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 375) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: N[C@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O) `ZINC001184484263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001184484263 none N[C@H](CSSC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)O)C(=O)O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'S.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 14, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 1, 11, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 5, 4, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 12, 12, 9, 7, 3, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 8, 8, 31, 31, 31, 31, 31, 31, 31, 9, 9, 3, 4, 4, 4, 4, 24, 93] 450 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: 251 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001184484263 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001184484263 Building ZINC000010097116 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000010097116 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/376 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000010097116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000010097116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000010097116 none Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 27, 27, 6, 3, 6, 6, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 3, 3, 27, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 3, 3, 3, 3] 46 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/377 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000010097116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000010097116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000010097116 none Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 28, 5, 3, 5, 5, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 3, 3, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000010097116 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 Building ZINC000010097116 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000010097116 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 376) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000010097116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000010097116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000010097116 none Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 27, 27, 6, 3, 6, 6, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 3, 3, 27, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 3, 3, 3, 3] 46 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 377) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000010097116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000010097116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000010097116 none Cc1noc(C)c1S(=O)(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 28, 5, 3, 5, 5, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 3, 3, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000010097116 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000010097116 Building ZINC000011327635 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011327635 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/378 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1) `ZINC000011327635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011327635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000011327635 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] 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, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 3, 12, 12, 32, 32, 34, 40, 40, 40, 40, 35, 12, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 12, 12, 9, 40, 40, 40, 40, 40, 40, 40, 40, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/379 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1) `ZINC000011327635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011327635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000011327635 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] 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, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 13, 10, 13, 13, 33, 33, 35, 41, 41, 41, 41, 35, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 41, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000011327635 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 Building ZINC000011327635 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011327635 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 378) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1) `ZINC000011327635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011327635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000011327635 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] 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, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 3, 12, 12, 32, 32, 34, 40, 40, 40, 40, 35, 12, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 12, 12, 9, 40, 40, 40, 40, 40, 40, 40, 40, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 379) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1) `ZINC000011327635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011327635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000011327635 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] 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, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 13, 10, 13, 13, 33, 33, 35, 41, 41, 41, 41, 35, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 41, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000011327635 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011327635 Building ZINC000011530430 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011530430 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/380 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000011530430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011530430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000011530430 none COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 13, 13, 16, 22, 22, 22, 22, 16, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/381 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000011530430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011530430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000011530430 none COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 12, 12, 15, 22, 22, 22, 22, 16, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000011530430 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 Building ZINC000011530430 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011530430 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 380) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000011530430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011530430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000011530430 none COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 13, 13, 16, 22, 22, 22, 22, 16, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 381) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000011530430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011530430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000011530430 none COc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 12, 12, 15, 22, 22, 22, 22, 16, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000011530430 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000011530430 Building ZINC000012267783 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012267783 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/382 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1) `ZINC000012267783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012267783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000012267783 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 7, 7, 7, 22, 22, 26, 32, 32, 32, 32, 28, 17, 17, 17, 7, 7, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 7, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/383 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1) `ZINC000012267783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012267783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000012267783 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 8, 8, 8, 25, 25, 33, 38, 38, 38, 38, 34, 18, 18, 18, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 8, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000012267783 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 Building ZINC000012267783 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012267783 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 382) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1) `ZINC000012267783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012267783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000012267783 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 7, 7, 7, 22, 22, 26, 32, 32, 32, 32, 28, 17, 17, 17, 7, 7, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 7, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 383) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1) `ZINC000012267783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012267783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000012267783 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 8, 8, 8, 25, 25, 33, 38, 38, 38, 38, 34, 18, 18, 18, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 8, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000012267783 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012267783 Building ZINC000012618426 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012618426 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/384 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/384' -> `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)N1CCN(Cc2cc(=O)n3ccsc3n2)CC1) `ZINC000012618426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012618426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012618426 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cc(=O)n3ccsc3n2)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', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 11, 8, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 6, 6, 6, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 6, 6, 6, 14, 14, 31, 31, 31, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/385 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/385' -> `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)N1CCN(Cc2cc(=O)n3ccsc3n2)CC1) `ZINC000012618426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012618426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012618426 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cc(=O)n3ccsc3n2)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', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 11, 8, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 6, 6, 6, 6, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 6, 6, 6, 6, 15, 15, 36, 36, 36, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000012618426 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 Building ZINC000012618426 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012618426 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 384) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cc(=O)n3ccsc3n2)CC1) `ZINC000012618426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012618426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012618426 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cc(=O)n3ccsc3n2)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', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 11, 8, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 6, 6, 6, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 6, 6, 6, 14, 14, 31, 31, 31, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 385) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cc(=O)n3ccsc3n2)CC1) `ZINC000012618426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012618426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012618426 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cc(=O)n3ccsc3n2)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', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 11, 8, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 6, 6, 6, 6, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 6, 6, 6, 6, 15, 15, 36, 36, 36, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000012618426 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012618426 Building ZINC000012627168 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012627168 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/386 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/386' -> `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)NCc1ccccc1CS(=O)(=O)N1CCOCC1) `ZINC000012627168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012627168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012627168 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CS(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 13, 13, 13, 13, 13, 13, 13, 23, 23, 27, 37, 37, 37, 37, 30, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 11, 11, 13, 13, 13, 13, 13, 13, 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/387 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/387' -> `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)NCc1ccccc1CS(=O)(=O)N1CCOCC1) `ZINC000012627168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012627168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012627168 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CS(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 14, 14, 14, 14, 14, 14, 16, 24, 24, 28, 38, 38, 38, 38, 30, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 10, 10, 14, 14, 14, 14, 16, 16, 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000012627168 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 Building ZINC000012627168 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012627168 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 386) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CS(=O)(=O)N1CCOCC1) `ZINC000012627168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012627168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012627168 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CS(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 13, 13, 13, 13, 13, 13, 13, 23, 23, 27, 37, 37, 37, 37, 30, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 11, 11, 13, 13, 13, 13, 13, 13, 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: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 387) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CS(=O)(=O)N1CCOCC1) `ZINC000012627168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012627168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000012627168 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CS(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 14, 14, 14, 14, 14, 14, 16, 24, 24, 28, 38, 38, 38, 38, 30, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 10, 10, 14, 14, 14, 14, 16, 16, 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: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000012627168 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000012627168 Building ZINC000016224814 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016224814 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/388 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/388' -> `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)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1) `ZINC000016224814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016224814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000016224814 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 5, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 10, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 93 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/389 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/389' -> `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)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1) `ZINC000016224814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016224814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000016224814 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 5, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 10, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 95 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016224814 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 Building ZINC000016224814 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016224814 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 388) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1) `ZINC000016224814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016224814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000016224814 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 5, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 10, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 93 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 389) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1) `ZINC000016224814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016224814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000016224814 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(C)c(C)c(C)c(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 5, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 10, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 95 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016224814 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016224814 Building ZINC000016227419 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016227419 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/390 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1) `ZINC000016227419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016227419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016227419 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 20, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 20, 46, 46, 46, 46, 46, 46, 46, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/391 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1) `ZINC000016227419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016227419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016227419 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 17, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 17, 46, 46, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016227419 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 Building ZINC000016227419 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016227419 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 390) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1) `ZINC000016227419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016227419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016227419 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 20, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 20, 46, 46, 46, 46, 46, 46, 46, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 391) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1) `ZINC000016227419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016227419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016227419 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 17, 26, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 17, 46, 46, 46, 46, 46, 46, 46, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016227419 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227419 Building ZINC000016227785 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016227785 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/392 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/392' -> `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)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1) `ZINC000016227785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016227785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016227785 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 9, 18, 18, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 34, 34, 34, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/393 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/393' -> `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)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1) `ZINC000016227785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016227785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016227785 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 21, 21, 21, 21, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 38, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016227785 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 Building ZINC000016227785 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016227785 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 392) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1) `ZINC000016227785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016227785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016227785 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 9, 18, 18, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 34, 34, 34, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 393) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1) `ZINC000016227785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016227785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016227785 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(Cl)cccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 21, 21, 21, 21, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 38, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016227785 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016227785 Building ZINC000016230974 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016230974 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/394 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/394' -> `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)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1) `ZINC000016230974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016230974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016230974 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 18, 18, 18, 36, 36, 34, 36, 36, 36, 36, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 36, 36, 36, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/395 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/395' -> `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)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1) `ZINC000016230974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016230974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016230974 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 19, 19, 19, 35, 35, 34, 35, 35, 35, 35, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 35, 35, 35, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016230974 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 Building ZINC000016230974 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016230974 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 394) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1) `ZINC000016230974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016230974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016230974 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 18, 18, 18, 36, 36, 34, 36, 36, 36, 36, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 36, 36, 36, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 395) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1) `ZINC000016230974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016230974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016230974 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 19, 19, 19, 35, 35, 34, 35, 35, 35, 35, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 35, 35, 35, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016230974 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016230974 Building ZINC000016231017 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231017 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/396 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/396' -> `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)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1) `ZINC000016231017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231017 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 5, 10, 10, 10, 10, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 35, 35, 35, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/397 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/397' -> `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)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1) `ZINC000016231017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231017 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 34, 34, 34, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231017 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 Building ZINC000016231017 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231017 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 396) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1) `ZINC000016231017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231017 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 5, 10, 10, 10, 10, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 35, 35, 35, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 397) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1) `ZINC000016231017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231017 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(Cl)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 34, 34, 34, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231017 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231017 Building ZINC000016231083 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231083 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/398 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/398' -> `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)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1) `ZINC000016231083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231083 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 18, 18, 18, 37, 37, 32, 37, 37, 37, 37, 37, 37, 37, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 37, 37, 37, 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, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/399 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/399' -> `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)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1) `ZINC000016231083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231083 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 19, 19, 19, 37, 37, 19, 25, 37, 37, 37, 37, 37, 37, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 37, 37, 37, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231083 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 Building ZINC000016231083 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231083 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 398) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1) `ZINC000016231083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231083 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 18, 18, 18, 37, 37, 32, 37, 37, 37, 37, 37, 37, 37, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 37, 37, 37, 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, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 399) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1) `ZINC000016231083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231083 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(Cl)c(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 19, 19, 19, 37, 37, 19, 25, 37, 37, 37, 37, 37, 37, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 37, 37, 37, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231083 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231083 Building ZINC000016231116 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231116 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/400 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/400' -> `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)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1) `ZINC000016231116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231116 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 11, 11, 11, 11, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 36, 36, 36, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/401 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/401' -> `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)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1) `ZINC000016231116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231116 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 24, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 34, 34, 34, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231116 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 Building ZINC000016231116 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231116 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 400) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1) `ZINC000016231116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231116 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 11, 11, 11, 11, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 36, 36, 36, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 401) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1) `ZINC000016231116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231116 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc(C(F)(F)F)ccc2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 24, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 34, 34, 34, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231116 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231116 Building ZINC000016231137 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231137 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/402 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1) `ZINC000016231137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231137 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 5, 10, 10, 10, 10, 19, 19, 19, 35, 35, 35, 35, 35, 35, 35, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 35, 35, 35, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/403 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1) `ZINC000016231137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231137 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 36, 36, 36, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231137 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 Building ZINC000016231137 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016231137 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 402) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1) `ZINC000016231137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016231137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231137 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 5, 10, 10, 10, 10, 19, 19, 19, 35, 35, 35, 35, 35, 35, 35, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 35, 35, 35, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 403) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1) `ZINC000016231137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016231137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000016231137 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cccc(Cl)c2Cl)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 36, 36, 36, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016231137 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016231137 Building ZINC000016699725 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016699725 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/404 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/404' -> `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)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1) `ZINC000016699725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000016699725 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 32, 32, 32, 37, 37, 33, 33, 37, 37, 18, 18, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 2, 18, 18, 18, 18, 37, 37, 37, 37, 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]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/405 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/405' -> `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)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1) `ZINC000016699725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000016699725 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 28, 28, 28, 32, 32, 30, 30, 32, 32, 16, 16, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 16, 16, 16, 16, 32, 32, 32, 32, 16, 16, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016699725 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 Building ZINC000016699725 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016699725 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 404) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1) `ZINC000016699725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000016699725 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 32, 32, 32, 37, 37, 33, 33, 37, 37, 18, 18, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 2, 18, 18, 18, 18, 37, 37, 37, 37, 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]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 405) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1) `ZINC000016699725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000016699725 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 28, 28, 28, 32, 32, 30, 30, 32, 32, 16, 16, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 16, 16, 16, 16, 32, 32, 32, 32, 16, 16, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000016699725 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000016699725 Building ZINC000017053260 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017053260 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/406 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/406' -> `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)N1CCN(S(=O)(=O)c2ccccc2)CC1) `ZINC000017053260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017053260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017053260 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 8, 16, 16, 16, 16, 27, 27, 27, 39, 39, 38, 39, 39, 16, 16, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 16, 16, 16, 16, 39, 39, 38, 39, 39, 16, 16, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/407 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/407' -> `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)N1CCN(S(=O)(=O)c2ccccc2)CC1) `ZINC000017053260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017053260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017053260 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 26, 26, 26, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000017053260 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 Building ZINC000017053260 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017053260 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 406) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccccc2)CC1) `ZINC000017053260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017053260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017053260 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 8, 16, 16, 16, 16, 27, 27, 27, 39, 39, 38, 39, 39, 16, 16, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 16, 16, 16, 16, 39, 39, 38, 39, 39, 16, 16, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 407) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccccc2)CC1) `ZINC000017053260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017053260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017053260 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 26, 26, 26, 33, 33, 33, 33, 33, 14, 14, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 14, 14, 14, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000017053260 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017053260 Building ZINC000017847056 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017847056 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/408 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/408' -> `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)N1CCN(S(=O)(=O)Cc2ccccc2)CC1) `ZINC000017847056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017847056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017847056 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 13, 13, 13, 13, 19, 19, 19, 35, 36, 36, 36, 36, 36, 13, 13, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 13, 13, 13, 13, 35, 35, 36, 36, 36, 36, 36, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/409 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/409' -> `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)N1CCN(S(=O)(=O)Cc2ccccc2)CC1) `ZINC000017847056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017847056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017847056 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 17, 17, 17, 34, 37, 37, 34, 37, 37, 9, 9, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 9, 9, 9, 9, 34, 34, 37, 37, 34, 37, 37, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000017847056 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 Building ZINC000017847056 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017847056 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 408) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)Cc2ccccc2)CC1) `ZINC000017847056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017847056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017847056 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 13, 13, 13, 13, 19, 19, 19, 35, 36, 36, 36, 36, 36, 13, 13, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 13, 13, 13, 13, 35, 35, 36, 36, 36, 36, 36, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 409) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)Cc2ccccc2)CC1) `ZINC000017847056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017847056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000017847056 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 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] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 17, 17, 17, 34, 37, 37, 34, 37, 37, 9, 9, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 9, 9, 9, 9, 34, 34, 37, 37, 34, 37, 37, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000017847056 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017847056 Building ZINC000017961821 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017961821 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/410 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000017961821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017961821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000017961821 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 39, 17, 38, 38, 17, 13, 17, 17, 13, 13, 13, 4, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 13, 13, 38, 38, 39, 39, 39, 38, 38, 13, 13, 13, 13, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 13, 13, 13, 13, 38, 38] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/411 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000017961821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017961821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000017961821 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 14, 30, 30, 14, 8, 14, 14, 8, 8, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 30, 30, 32, 32, 32, 30, 30, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 8, 8, 30, 30] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000017961821 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 Building ZINC000017961821 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017961821 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 410) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000017961821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017961821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000017961821 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 39, 17, 38, 38, 17, 13, 17, 17, 13, 13, 13, 4, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 13, 13, 38, 38, 39, 39, 39, 38, 38, 13, 13, 13, 13, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 13, 13, 13, 13, 38, 38] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 411) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000017961821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017961821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000017961821 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 14, 30, 30, 14, 8, 14, 14, 8, 8, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 30, 30, 32, 32, 32, 30, 30, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 8, 8, 30, 30] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000017961821 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000017961821 Building ZINC000018151771 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018151771 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/412 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)cc1) `ZINC000018151771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018151771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000018151771 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 13, 25, 25, 16, 18, 43, 43, 43, 50, 50, 50, 50, 43, 25, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/413 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)cc1) `ZINC000018151771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018151771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000018151771 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 17, 19, 43, 43, 43, 48, 48, 48, 48, 43, 24, 24, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 24, 24, 48, 48, 48, 48, 48, 48, 48, 48, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000018151771 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 Building ZINC000018151771 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018151771 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 412) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)cc1) `ZINC000018151771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018151771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000018151771 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 13, 25, 25, 16, 18, 43, 43, 43, 50, 50, 50, 50, 43, 25, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 413) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)cc1) `ZINC000018151771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018151771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000018151771 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)N2CCOCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 17, 19, 43, 43, 43, 48, 48, 48, 48, 43, 24, 24, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 24, 24, 48, 48, 48, 48, 48, 48, 48, 48, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000018151771 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000018151771 Building ZINC000021632458 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000021632458 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/414 `/scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NCc2ccccc2)CC1) `ZINC000021632458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000021632458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000021632458 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NCc2ccccc2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 5, 5, 5, 10, 12, 12, 12, 28, 31, 31, 28, 31, 31, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 10, 10, 12, 28, 28, 31, 31, 28, 31, 31, 5, 5, 5, 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, 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/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/415 `/scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NCc2ccccc2)CC1) `ZINC000021632458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000021632458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000021632458 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NCc2ccccc2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 6, 9, 9, 9, 31, 34, 34, 31, 34, 34, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 31, 31, 34, 34, 31, 34, 34, 2, 2, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000021632458 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 Building ZINC000021632458 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000021632458 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 414) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NCc2ccccc2)CC1) `ZINC000021632458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000021632458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000021632458 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NCc2ccccc2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 5, 5, 5, 10, 12, 12, 12, 28, 31, 31, 28, 31, 31, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 10, 10, 12, 28, 28, 31, 31, 28, 31, 31, 5, 5, 5, 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, 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/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 415) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NCc2ccccc2)CC1) `ZINC000021632458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000021632458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000021632458 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NCc2ccccc2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 6, 9, 9, 9, 31, 34, 34, 31, 34, 34, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 31, 31, 34, 34, 31, 34, 34, 2, 2, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/194367/xbs-8058088.45/working/building/ZINC000021632458 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000021632458 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021632458 Building ZINC000021874679 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000021874679 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/416 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000021874679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000021874679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000021874679 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 22, 37, 37, 22, 14, 22, 22, 14, 14, 14, 4, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 14, 14, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 14, 14, 14, 14, 37, 37] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/417 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000021874679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000021874679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000021874679 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 31, 31, 21, 10, 21, 21, 10, 10, 10, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 10, 10, 10, 10, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000021874679 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 Building ZINC000021874679 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000021874679 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 416) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000021874679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000021874679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000021874679 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 22, 37, 37, 22, 14, 22, 22, 14, 14, 14, 4, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 14, 14, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 14, 14, 14, 14, 37, 37] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 417) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC000021874679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000021874679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000021874679 none COc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 31, 31, 21, 10, 21, 21, 10, 10, 10, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 10, 10, 10, 10, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000021874679 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000021874679 Building ZINC000024779600 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000024779600 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/418 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1) `ZINC000024779600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000024779600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000024779600 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 8, 8, 8, 8, 8, 11, 11, 11, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8, 8, 8, 11, 11, 11, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/419 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1) `ZINC000024779600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000024779600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000024779600 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 8, 8, 8, 8, 8, 8, 12, 12, 12, 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]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000024779600 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 Building ZINC000024779600 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000024779600 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 418) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1) `ZINC000024779600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000024779600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000024779600 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 8, 8, 8, 8, 8, 11, 11, 11, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8, 8, 8, 11, 11, 11, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 419) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1) `ZINC000024779600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000024779600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000024779600 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 8, 8, 8, 8, 8, 8, 12, 12, 12, 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]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000024779600 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000024779600 Building ZINC000025133665 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000025133665 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/420 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/420' -> `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)NCCNS(=O)(=O)c1cccc(Cl)c1) `ZINC000025133665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000025133665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000025133665 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 13, 23, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 13, 13, 23, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/421 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/421' -> `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)NCCNS(=O)(=O)c1cccc(Cl)c1) `ZINC000025133665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000025133665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000025133665 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 13, 23, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 13, 13, 23, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000025133665 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 Building ZINC000025133665 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000025133665 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 420) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc(Cl)c1) `ZINC000025133665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000025133665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000025133665 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 13, 23, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 13, 13, 23, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 421) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc(Cl)c1) `ZINC000025133665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000025133665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000025133665 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 13, 23, 35, 35, 35, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 13, 13, 23, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000025133665 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000025133665 Building ZINC000028026173 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028026173 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/422 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/422' -> `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)N1CCN(CC(=O)NC2CC2)CC1) `ZINC000028026173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028026173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000028026173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 8, 10, 10, 10, 13, 13, 5, 5, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 5, 5, 5, 5, 8, 8, 10, 13, 13, 13, 13, 13, 5, 5, 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, 59]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/423 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/423' -> `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)N1CCN(CC(=O)NC2CC2)CC1) `ZINC000028026173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028026173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000028026173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 8, 10, 10, 10, 14, 14, 5, 5, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 5, 5, 5, 5, 8, 8, 10, 14, 14, 14, 14, 14, 5, 5, 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, 59]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000028026173 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 Building ZINC000028026173 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028026173 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 422) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CC2)CC1) `ZINC000028026173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028026173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000028026173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 8, 10, 10, 10, 13, 13, 5, 5, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 5, 5, 5, 5, 8, 8, 10, 13, 13, 13, 13, 13, 5, 5, 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, 59]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 423) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CC2)CC1) `ZINC000028026173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028026173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000028026173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 8, 10, 10, 10, 14, 14, 5, 5, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 5, 5, 5, 5, 8, 8, 10, 14, 14, 14, 14, 14, 5, 5, 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, 59]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000028026173 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028026173 Building ZINC000028326113 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028326113 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/424 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)CC1) `ZINC000028326113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028326113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000028326113 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 6, 6, 23, 35, 35, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/425 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)CC1) `ZINC000028326113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028326113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000028326113 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 21, 37, 38, 39, 39, 39, 39, 39, 39, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000028326113 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 Building ZINC000028326113 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000028326113 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 424) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)CC1) `ZINC000028326113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000028326113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000028326113 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 6, 6, 23, 35, 35, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 425) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)CC1) `ZINC000028326113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000028326113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000028326113 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 21, 37, 38, 39, 39, 39, 39, 39, 39, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 14, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000028326113 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000028326113 Building ZINC000029363057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029363057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/426 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/426' -> `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)N1CCN(CC(=O)N2CCCC[C@H]2C)CC1) `ZINC000029363057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029363057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363057 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 14, 26, 26, 31, 31, 31, 31, 31, 31, 31, 5, 5, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 5, 5, 5, 5, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 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, 62, 63, 64, 65]) total number of confs: 111 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/427 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/427' -> `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)N1CCN(CC(=O)N2CCCC[C@H]2C)CC1) `ZINC000029363057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029363057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363057 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 5, 5, 5, 5, 12, 33, 33, 36, 36, 36, 36, 36, 36, 36, 5, 5, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 5, 5, 5, 5, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 5, 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, 62, 63, 64, 65]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000029363057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 Building ZINC000029363057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029363057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 426) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@H]2C)CC1) `ZINC000029363057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029363057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363057 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 14, 26, 26, 31, 31, 31, 31, 31, 31, 31, 5, 5, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 5, 5, 5, 5, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 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, 62, 63, 64, 65]) total number of confs: 111 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 427) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@H]2C)CC1) `ZINC000029363057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029363057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363057 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 4, 5, 5, 5, 5, 12, 33, 33, 36, 36, 36, 36, 36, 36, 36, 5, 5, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 5, 5, 5, 5, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 5, 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, 62, 63, 64, 65]) total number of confs: 125 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000029363057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363057 Building ZINC000029363058 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029363058 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/428 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)CC1) `ZINC000029363058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029363058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363058 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 6, 6, 6, 14, 30, 30, 34, 34, 34, 34, 34, 34, 34, 6, 6, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 6, 6, 6, 6, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/429 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)CC1) `ZINC000029363058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029363058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363058 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 14, 32, 32, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6, 14, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000029363058 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 Building ZINC000029363058 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029363058 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 428) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)CC1) `ZINC000029363058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029363058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363058 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 6, 6, 6, 14, 30, 30, 34, 34, 34, 34, 34, 34, 34, 6, 6, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 6, 6, 6, 6, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 120 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 429) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)CC1) `ZINC000029363058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029363058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000029363058 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC[C@@H]2C)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 14, 32, 32, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6, 14, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000029363058 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029363058 Building ZINC000029669604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029669604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/430 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/430' -> `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)N1CCN(C(=O)c2ccc3c(c2)OCO3)CC1) `ZINC000029669604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029669604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029669604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccc3c(c2)OCO3)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/431 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/431' -> `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)N1CCN(C(=O)c2ccc3c(c2)OCO3)CC1) `ZINC000029669604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029669604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029669604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccc3c(c2)OCO3)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000029669604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 Building ZINC000029669604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029669604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 430) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccc3c(c2)OCO3)CC1) `ZINC000029669604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029669604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029669604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccc3c(c2)OCO3)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 431) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccc3c(c2)OCO3)CC1) `ZINC000029669604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029669604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029669604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccc3c(c2)OCO3)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 6, 6, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000029669604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000029669604 Building ZINC000031349617 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000031349617 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/432 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/432' -> `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)N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1) `ZINC000031349617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000031349617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000031349617 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(F)cccc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 15, 15, 15, 15, 24, 24, 24, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/433 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/433' -> `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)N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1) `ZINC000031349617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000031349617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000031349617 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(F)cccc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 12, 12, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 12, 12, 12, 12, 32, 32, 32, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000031349617 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 Building ZINC000031349617 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000031349617 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 432) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1) `ZINC000031349617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000031349617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000031349617 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(F)cccc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 15, 15, 15, 15, 24, 24, 24, 37, 37, 37, 37, 37, 37, 37, 15, 15, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 433) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1) `ZINC000031349617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000031349617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000031349617 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c(F)cccc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 12, 12, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 12, 12, 12, 12, 32, 32, 32, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000031349617 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000031349617 Building ZINC000032395693 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000032395693 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/434 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000032395693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000032395693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000032395693 none CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 22, 28, 22, 22, 22, 10, 10, 10, 10, 8, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 22, 22, 43, 43, 43, 43, 43, 22, 22, 22, 22, 22, 10, 9, 10, 9, 9, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 22, 22] 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, 63, 64, 65, 66, 67]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/435 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000032395693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000032395693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000032395693 none CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 20, 32, 20, 20, 20, 12, 12, 12, 12, 8, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 20, 20, 47, 47, 47, 47, 47, 20, 20, 20, 20, 20, 12, 12, 11, 10, 10, 7, 7, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 20, 20, 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000032395693 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 Building ZINC000032395693 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000032395693 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 434) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000032395693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000032395693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000032395693 none CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 22, 28, 22, 22, 22, 10, 10, 10, 10, 8, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 22, 22, 43, 43, 43, 43, 43, 22, 22, 22, 22, 22, 10, 9, 10, 9, 9, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22, 22, 22, 22] 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, 63, 64, 65, 66, 67]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 435) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1) `ZINC000032395693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000032395693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000032395693 none CCOC(=O)N1CCC(NC(=O)CCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 20, 32, 20, 20, 20, 12, 12, 12, 12, 8, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 20, 20, 47, 47, 47, 47, 47, 20, 20, 20, 20, 20, 12, 12, 11, 10, 10, 7, 7, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 20, 20, 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000032395693 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000032395693 Building ZINC000105464887 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105464887 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/436 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/436' -> `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(S(=O)(=O)N2CCN(C)CC2)cc1) `ZINC000105464887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105464887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105464887 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 2, 21, 21, 26, 39, 39, 39, 39, 39, 28, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/437 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/437' -> `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(S(=O)(=O)N2CCN(C)CC2)cc1) `ZINC000105464887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105464887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105464887 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 22, 22, 27, 43, 43, 43, 43, 43, 29, 5, 5, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000105464887 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 Building ZINC000105464887 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105464887 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 436) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1) `ZINC000105464887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105464887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105464887 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 2, 21, 21, 26, 39, 39, 39, 39, 39, 28, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 437) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1) `ZINC000105464887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105464887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105464887 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 22, 22, 27, 43, 43, 43, 43, 43, 29, 5, 5, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000105464887 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105464887 Building ZINC000105494387 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105494387 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/438 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O) `ZINC000105494387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105494387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000105494387 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 11, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 3, 3, 1, 1, 1, 1, 4, 4, 9, 10, 10, 10, 9, 16, 16, 16, 16, 21, 21, 21, 16, 16, 16, 16, 16, 16, 3, 3, 3, 13, 13, 3, 13, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 103 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/439 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O) `ZINC000105494387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105494387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000105494387 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 11, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 5, 5, 9, 10, 10, 10, 9, 17, 17, 17, 17, 27, 27, 27, 17, 17, 17, 17, 17, 17, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 128 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000105494387 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 Building ZINC000105494387 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105494387 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 438) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O) `ZINC000105494387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105494387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000105494387 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 11, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 3, 3, 1, 1, 1, 1, 4, 4, 9, 10, 10, 10, 9, 16, 16, 16, 16, 21, 21, 21, 16, 16, 16, 16, 16, 16, 3, 3, 3, 13, 13, 3, 13, 13, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 103 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 439) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O) `ZINC000105494387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105494387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000105494387 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)c1c(N)n(CC(C)C)c(=O)[nH]c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 5, 5, 5, 1, 11, 8, 6, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 5, 5, 9, 10, 10, 10, 9, 17, 17, 17, 17, 27, 27, 27, 17, 17, 17, 17, 17, 17, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 128 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000105494387 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000105494387 Building ZINC000106316011 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106316011 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/440 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000106316011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106316011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000106316011 none CCS(=O)(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 14, 14, 9, 13, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 14, 14, 14, 14, 14, 13, 13, 13, 9, 9, 9, 9, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 46, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/441 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000106316011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106316011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000106316011 none CCS(=O)(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 11, 12, 12, 10, 11, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 12, 12, 12, 12, 12, 11, 11, 11, 10, 10, 9, 9, 6, 6, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 46, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000106316011 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 Building ZINC000106316011 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106316011 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 440) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCS(=O)(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000106316011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106316011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000106316011 none CCS(=O)(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 14, 14, 9, 13, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 14, 14, 14, 14, 14, 13, 13, 13, 9, 9, 9, 9, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 46, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 441) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCS(=O)(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000106316011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106316011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000106316011 none CCS(=O)(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 11, 12, 12, 10, 11, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 12, 12, 12, 12, 12, 11, 11, 11, 10, 10, 9, 9, 6, 6, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 46, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000106316011 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000106316011 Building ZINC000108659809 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108659809 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/442 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/442' -> `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)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)CC1) `ZINC000108659809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108659809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000108659809 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 8, 6, 1, 8, 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] 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, 6, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 17, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 11, 11, 11, 11, 41, 41, 41, 41, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/443 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/443' -> `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)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)CC1) `ZINC000108659809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108659809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000108659809 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 8, 6, 1, 8, 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] 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, 6, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 16, 16, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 6, 6, 6, 6, 35, 35, 35, 35, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000108659809 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 Building ZINC000108659809 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108659809 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 442) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)CC1) `ZINC000108659809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108659809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000108659809 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 8, 6, 1, 8, 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] 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, 6, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 17, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 11, 11, 11, 11, 41, 41, 41, 41, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 443) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)CC1) `ZINC000108659809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108659809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000108659809 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2c[nH]c3ncccc23)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 8, 6, 1, 8, 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] 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, 6, 6, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 16, 16, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 6, 6, 6, 6, 35, 35, 35, 35, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000108659809 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000108659809 Building ZINC000109386723 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000109386723 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/444 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000109386723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109386723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000109386723 none COCCCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 13, 11, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 22, 22, 22, 19, 19, 13, 13, 11, 11, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/445 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000109386723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109386723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000109386723 none COCCCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 13, 11, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 22, 22, 22, 19, 19, 13, 13, 11, 11, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000109386723 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 Building ZINC000109386723 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000109386723 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 444) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000109386723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109386723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000109386723 none COCCCNC(=O)CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 13, 11, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 22, 22, 22, 19, 19, 13, 13, 11, 11, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 445) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000109386723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109386723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000109386723 none COCCCNC(=O)CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 13, 11, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 22, 22, 22, 19, 19, 13, 13, 11, 11, 5, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000109386723 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000109386723 Building ZINC000113491165 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491165 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/446 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491165 none O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 11, 12, 12, 12, 12, 12, 2, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 12, 12, 12, 12, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/447 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491165 none O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 10, 20, 20, 20, 20, 20, 3, 10, 10, 10, 10, 10, 10, 10, 15, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 20, 10, 10, 10, 10, 15, 15, 16, 16, 16, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491165 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 Building ZINC000113491165 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491165 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 446) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491165 none O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 11, 12, 12, 12, 12, 12, 2, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 12, 12, 12, 12, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 447) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491165 none O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 10, 20, 20, 20, 20, 20, 3, 10, 10, 10, 10, 10, 10, 10, 15, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 20, 10, 10, 10, 10, 15, 15, 16, 16, 16, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491165 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491165 Building ZINC000113491167 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491167 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/448 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491167 none O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 4, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 17, 17, 17, 17, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/449 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491167 none O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 12, 13, 13, 13, 13, 13, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 13, 13, 13, 13, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 24] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491167 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 Building ZINC000113491167 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491167 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 448) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491167 none O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 4, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 17, 17, 17, 17, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 449) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491167 none O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 12, 13, 13, 13, 13, 13, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 13, 13, 13, 13, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 24] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491167 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491167 Building ZINC000113491169 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491169 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/450 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491169 none O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 24] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/451 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491169 none O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 10, 17, 17, 17, 17, 17, 4, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 17, 17, 17, 17, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491169 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 Building ZINC000113491169 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491169 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 450) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491169 none O=C(N[C@@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 24] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 451) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491169 none O=C(N[C@@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 10, 17, 17, 17, 17, 17, 4, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 17, 17, 17, 17, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491169 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491169 Building ZINC000113491170 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491170 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/452 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491170 none O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 10, 20, 20, 20, 20, 20, 3, 10, 10, 10, 10, 10, 10, 10, 15, 16, 16, 15, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 20, 10, 10, 10, 10, 15, 15, 16, 16, 15, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/453 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491170 none O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 11, 12, 12, 12, 12, 12, 2, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 12, 12, 12, 12, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491170 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 Building ZINC000113491170 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113491170 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 452) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113491170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491170 none O=C(N[C@H](Cc1ccccc1)[C@@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 10, 20, 20, 20, 20, 20, 3, 10, 10, 10, 10, 10, 10, 10, 15, 16, 16, 15, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 20, 10, 10, 10, 10, 15, 15, 16, 16, 15, 16, 16] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 453) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1) `ZINC000113491170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113491170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000113491170 none O=C(N[C@H](Cc1ccccc1)[C@]([O-])([SiH3])C(=O)NCc1ccccn1)[C@H]1CCC(=O)N1Cc1ccccc1 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', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 6, 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: [6, 7, 4, 9, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 11, 12, 12, 12, 12, 12, 2, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 2, 3, 3, 3, 3, 3, 3, 3, 2, 11, 11, 12, 12, 12, 12, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [3, 12, 13, 14] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000113491170 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000113491170 Building ZINC000116976171 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000116976171 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/454 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/454' -> `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)NCCCN(C)S(C)(=O)=O) `ZINC000116976171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000116976171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000116976171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 5, 14, 5, 11, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/455 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/455' -> `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)NCCCN(C)S(C)(=O)=O) `ZINC000116976171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000116976171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000116976171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 5, 14, 5, 11, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000116976171 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 Building ZINC000116976171 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000116976171 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 454) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN(C)S(C)(=O)=O) `ZINC000116976171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000116976171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000116976171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 5, 14, 5, 11, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 455) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN(C)S(C)(=O)=O) `ZINC000116976171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000116976171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000116976171 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 5, 14, 5, 11, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000116976171 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000116976171 Building ZINC000195552389 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195552389 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/456 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/456' -> `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)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1) `ZINC000195552389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195552389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000195552389 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 2, 4, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 5, 5, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1] 50 rigid atoms, others: [32, 45, 43, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 44, 61, 59, 60, 42, 62, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/457 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/457' -> `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)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1) `ZINC000195552389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195552389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000195552389 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 2, 2, 4, 6, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 10, 10, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000195552389 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 Building ZINC000195552389 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195552389 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 456) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1) `ZINC000195552389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195552389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000195552389 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 2, 4, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 5, 5, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1] 50 rigid atoms, others: [32, 45, 43, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 44, 61, 59, 60, 42, 62, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 457) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1) `ZINC000195552389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195552389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000195552389 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCCc2nc(c3ccc(C)cc3)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 2, 2, 2, 2, 4, 6, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 10, 10, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000195552389 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000195552389 Building ZINC000410000431 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410000431 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/458 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1) `ZINC000410000431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410000431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000431 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 9, 9, 9, 14, 14, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/459 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1) `ZINC000410000431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410000431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000431 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 10, 10, 12, 12, 12, 12, 12, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000410000431 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 Building ZINC000410000431 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410000431 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 458) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1) `ZINC000410000431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410000431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000431 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 9, 9, 9, 14, 14, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 459) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1) `ZINC000410000431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410000431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000431 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 10, 10, 12, 12, 12, 12, 12, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 3, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000410000431 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000431 Building ZINC000410000438 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410000438 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/460 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1) `ZINC000410000438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410000438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 11, 11, 17, 17, 17, 17, 17, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/461 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1) `ZINC000410000438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410000438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 13, 13, 17, 17, 17, 17, 17, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 5, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000410000438 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 Building ZINC000410000438 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410000438 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 460) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1) `ZINC000410000438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410000438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 11, 11, 17, 17, 17, 17, 17, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 461) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1) `ZINC000410000438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410000438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410000438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 13, 13, 17, 17, 17, 17, 17, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 5, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000410000438 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000410000438 Building ZINC000482677544 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482677544 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/462 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)CC2)cc1) `ZINC000482677544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482677544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482677544 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 29, 29, 15, 29, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 15, 15, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/463 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)CC2)cc1) `ZINC000482677544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482677544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482677544 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 27, 27, 16, 27, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 14, 14, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000482677544 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 Building ZINC000482677544 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482677544 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 462) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)CC2)cc1) `ZINC000482677544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482677544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482677544 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 29, 29, 15, 29, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 15, 15, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 463) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)CC2)cc1) `ZINC000482677544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482677544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482677544 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(C(=O)N2CCN(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 27, 27, 16, 27, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 14, 14, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000482677544 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482677544 Building ZINC000482811604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482811604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/464 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/464' -> `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(NC(=O)CCN2C(=O)CNC2=O)cc1) `ZINC000482811604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482811604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482811604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 7, 7, 7, 29, 30, 50, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 7, 29, 29, 30, 30, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/465 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/465' -> `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(NC(=O)CCN2C(=O)CNC2=O)cc1) `ZINC000482811604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482811604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482811604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 7, 7, 7, 30, 32, 50, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 7, 30, 30, 32, 32, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000482811604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 Building ZINC000482811604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000482811604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 464) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CCN2C(=O)CNC2=O)cc1) `ZINC000482811604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000482811604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482811604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 7, 7, 7, 29, 30, 50, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 7, 29, 29, 30, 30, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 465) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CCN2C(=O)CNC2=O)cc1) `ZINC000482811604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000482811604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000482811604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CCN2C(=O)CNC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 7, 7, 7, 30, 32, 50, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 7, 30, 30, 32, 32, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000482811604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000482811604 Building ZINC000487293163 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487293163 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/466 `/scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NC2CCCCC2)CC1) `ZINC000487293163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487293163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000487293163 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 7, 10, 10, 17, 33, 33, 33, 33, 33, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 7, 7, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/467 `/scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NC2CCCCC2)CC1) `ZINC000487293163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487293163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000487293163 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 4, 4, 9, 14, 14, 22, 39, 39, 39, 39, 39, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 9, 9, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 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, 62, 63, 64, 65]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000487293163 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 Building ZINC000487293163 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487293163 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 466) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NC2CCCCC2)CC1) `ZINC000487293163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487293163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000487293163 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 7, 10, 10, 17, 33, 33, 33, 33, 33, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 7, 7, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 467) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N1CCN(CC(=O)NC2CCCCC2)CC1) `ZINC000487293163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487293163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000487293163 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC2CCCCC2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 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, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 4, 4, 9, 14, 14, 22, 39, 39, 39, 39, 39, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 9, 9, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 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, 62, 63, 64, 65]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000487293163 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000487293163 Building ZINC000490568847 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490568847 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/468 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/468' -> `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)N1CCN(C(=O)CN2CCCC2)CC1) `ZINC000490568847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490568847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000490568847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CN2CCCC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 9, 9, 9, 9, 10, 10, 13, 13, 13, 13, 13, 9, 9, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/469 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/469' -> `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)N1CCN(C(=O)CN2CCCC2)CC1) `ZINC000490568847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490568847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000490568847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CN2CCCC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 8, 8, 10, 10, 10, 10, 10, 5, 5, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490568847 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 Building ZINC000490568847 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490568847 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 468) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CN2CCCC2)CC1) `ZINC000490568847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490568847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000490568847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CN2CCCC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 9, 9, 9, 9, 10, 10, 13, 13, 13, 13, 13, 9, 9, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 469) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CN2CCCC2)CC1) `ZINC000490568847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490568847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000490568847 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CN2CCCC2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 8, 8, 10, 10, 10, 10, 10, 5, 5, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490568847 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490568847 Building ZINC000490649857 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490649857 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/470 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)cc1) `ZINC000490649857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490649857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649857 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 22, 22, 24, 29, 29, 29, 29, 27, 8, 8, 8, 8, 19, 29, 37, 37, 37, 37, 37, 2, 2, 2, 2, 2, 2, 2, 3, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 19, 24, 24, 37, 37, 37, 37, 37, 37, 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, 62]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/471 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)cc1) `ZINC000490649857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490649857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649857 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 24, 24, 26, 28, 28, 28, 28, 26, 5, 8, 8, 8, 18, 27, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 3, 8, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 18, 22, 22, 35, 35, 35, 35, 35, 35, 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, 62]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490649857 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 Building ZINC000490649857 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490649857 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 470) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)cc1) `ZINC000490649857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490649857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649857 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 22, 22, 24, 29, 29, 29, 29, 27, 8, 8, 8, 8, 19, 29, 37, 37, 37, 37, 37, 2, 2, 2, 2, 2, 2, 2, 3, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 19, 24, 24, 37, 37, 37, 37, 37, 37, 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, 62]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 471) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)cc1) `ZINC000490649857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490649857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649857 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 24, 24, 26, 28, 28, 28, 28, 26, 5, 8, 8, 8, 18, 27, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 3, 8, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 18, 22, 22, 35, 35, 35, 35, 35, 35, 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, 62]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490649857 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649857 Building ZINC000490649872 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490649872 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/472 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)cc1) `ZINC000490649872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490649872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649872 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 23, 23, 25, 27, 27, 27, 27, 25, 5, 8, 8, 8, 18, 29, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 3, 8, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 18, 22, 22, 35, 35, 35, 35, 35, 35, 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, 62]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/473 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)cc1) `ZINC000490649872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490649872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649872 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 23, 23, 25, 29, 29, 29, 29, 27, 5, 8, 8, 8, 19, 30, 36, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 2, 3, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 19, 25, 25, 36, 36, 36, 36, 36, 36, 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, 62]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490649872 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 Building ZINC000490649872 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490649872 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 472) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)cc1) `ZINC000490649872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490649872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649872 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 23, 23, 25, 27, 27, 27, 27, 25, 5, 8, 8, 8, 18, 29, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2, 2, 3, 8, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 18, 22, 22, 35, 35, 35, 35, 35, 35, 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, 62]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 473) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)cc1) `ZINC000490649872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490649872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000490649872 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 23, 23, 25, 29, 29, 29, 29, 27, 5, 8, 8, 8, 19, 30, 36, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 2, 3, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 19, 25, 25, 36, 36, 36, 36, 36, 36, 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, 62]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490649872 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490649872 Building ZINC000490659942 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490659942 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/474 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000490659942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490659942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000490659942 none CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 16, 9, 5, 5, 5, 4, 5, 5, 10, 10, 11, 13, 13, 13, 13, 12, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 29, 29, 16, 16, 9, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/475 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000490659942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490659942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000490659942 none CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 17, 10, 5, 5, 5, 4, 5, 5, 11, 11, 12, 15, 15, 15, 15, 14, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 29, 29, 17, 17, 10, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490659942 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 Building ZINC000490659942 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490659942 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 474) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000490659942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490659942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000490659942 none CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 16, 9, 5, 5, 5, 4, 5, 5, 10, 10, 11, 13, 13, 13, 13, 12, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 29, 29, 16, 16, 9, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 475) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000490659942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490659942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000490659942 none CCCCNc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 17, 10, 5, 5, 5, 4, 5, 5, 11, 11, 12, 15, 15, 15, 15, 14, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 29, 29, 17, 17, 10, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000490659942 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000490659942 Building ZINC000497343580 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497343580 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/476 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/476' -> `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)N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1) `ZINC000497343580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497343580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497343580 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 14, 14, 14, 14, 20, 20, 20, 43, 43, 36, 41, 43, 43, 43, 14, 14, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 14, 14, 14, 14, 43, 43, 43, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/477 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/477' -> `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)N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1) `ZINC000497343580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497343580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497343580 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 18, 18, 18, 37, 37, 34, 36, 37, 37, 37, 9, 9, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 9, 9, 9, 9, 37, 37, 37, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497343580 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 Building ZINC000497343580 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497343580 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 476) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1) `ZINC000497343580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497343580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497343580 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 14, 14, 14, 14, 20, 20, 20, 43, 43, 36, 41, 43, 43, 43, 14, 14, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 14, 14, 14, 14, 43, 43, 43, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 477) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1) `ZINC000497343580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497343580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497343580 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2ccc(F)cc2F)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 18, 18, 18, 37, 37, 34, 36, 37, 37, 37, 9, 9, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 9, 9, 9, 9, 37, 37, 37, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497343580 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497343580 Building ZINC000497589653 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497589653 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/478 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000497589653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497589653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000497589653 none CCS(=O)(=O)NCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 13, 13, 13, 13, 13, 13, 7, 6, 6, 6, 5, 5, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 43, 44, 45, 46, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/479 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000497589653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497589653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000497589653 none CCS(=O)(=O)NCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 9, 7, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 16, 16, 16, 16, 16, 16, 8, 9, 8, 8, 5, 5, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2] 50 rigid atoms, others: [11, 8, 9, 10, 43, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497589653 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 Building ZINC000497589653 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497589653 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 478) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCS(=O)(=O)NCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000497589653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497589653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000497589653 none CCS(=O)(=O)NCCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 13, 13, 13, 13, 13, 13, 7, 6, 6, 6, 5, 5, 1, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 43, 44, 45, 46, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 479) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCS(=O)(=O)NCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000497589653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497589653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000497589653 none CCS(=O)(=O)NCCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 9, 7, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 16, 16, 16, 16, 16, 16, 8, 9, 8, 8, 5, 5, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2] 50 rigid atoms, others: [11, 8, 9, 10, 43, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497589653 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497589653 Building ZINC000497649195 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497649195 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/480 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/480' -> `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)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)CC1) `ZINC000497649195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497649195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649195 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 7, 7, 7, 7, 18, 24, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/481 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/481' -> `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)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)CC1) `ZINC000497649195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497649195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649195 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 6, 6, 19, 24, 24, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 120 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497649195 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 Building ZINC000497649195 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497649195 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 480) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)CC1) `ZINC000497649195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497649195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649195 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 7, 7, 7, 7, 18, 24, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 481) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)CC1) `ZINC000497649195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497649195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649195 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 6, 6, 19, 24, 24, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 120 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497649195 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649195 Building ZINC000497649197 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497649197 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/482 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)CC1) `ZINC000497649197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497649197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649197 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 7, 7, 7, 7, 23, 29, 29, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 7, 7, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 112 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/483 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)CC1) `ZINC000497649197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497649197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649197 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 7, 7, 7, 7, 23, 29, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 7, 7, 7, 7, 18, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497649197 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 Building ZINC000497649197 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497649197 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 482) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)CC1) `ZINC000497649197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497649197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649197 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 7, 7, 7, 7, 23, 29, 29, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 7, 7, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 112 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 483) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)CC1) `ZINC000497649197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497649197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649197 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@@H](C)C[C@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 7, 7, 7, 7, 23, 29, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 7, 7, 7, 7, 18, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497649197 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649197 Building ZINC000497649198 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497649198 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/484 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/484' -> `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)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)CC1) `ZINC000497649198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497649198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649198 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 7, 7, 7, 7, 23, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 7, 7, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 109 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/485 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/485' -> `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)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)CC1) `ZINC000497649198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497649198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649198 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 6, 6, 6, 6, 24, 32, 32, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 6, 6, 6, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 130 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497649198 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 Building ZINC000497649198 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497649198 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 484) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)CC1) `ZINC000497649198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497649198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649198 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 7, 7, 7, 7, 23, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 7, 7, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 109 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 485) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)CC1) `ZINC000497649198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497649198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000497649198 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2C[C@H](C)C[C@@H](C)C2)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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 6, 6, 6, 6, 24, 32, 32, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 6, 6, 6, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 130 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497649198 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497649198 Building ZINC000497802710 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497802710 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/486 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/486' -> `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)NCCCN1C(=O)NC2(CCCCC2)C1=O) `ZINC000497802710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497802710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497802710 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 16, 16, 18, 18, 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, 60, 61]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/487 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/487' -> `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)NCCCN1C(=O)NC2(CCCCC2)C1=O) `ZINC000497802710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497802710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497802710 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 15, 15, 16, 16, 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, 60, 61]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497802710 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 Building ZINC000497802710 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497802710 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 486) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)NC2(CCCCC2)C1=O) `ZINC000497802710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497802710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497802710 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 16, 16, 18, 18, 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, 60, 61]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 487) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)NC2(CCCCC2)C1=O) `ZINC000497802710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497802710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000497802710 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 14, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 15, 15, 16, 16, 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, 60, 61]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000497802710 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000497802710 Building ZINC000498047301 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498047301 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/488 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000498047301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498047301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498047301 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 10, 10, 10, 29, 36, 36, 36, 29, 36, 36, 36, 36, 4, 4, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 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, 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/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/489 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000498047301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498047301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498047301 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 6, 6, 6, 6, 10, 10, 10, 28, 37, 37, 37, 28, 37, 37, 37, 37, 6, 6, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4] 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, 58]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000498047301 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 Building ZINC000498047301 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498047301 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 488) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000498047301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498047301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498047301 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 10, 10, 10, 29, 36, 36, 36, 29, 36, 36, 36, 36, 4, 4, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 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, 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/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 489) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000498047301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498047301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498047301 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 6, 6, 6, 6, 10, 10, 10, 28, 37, 37, 37, 28, 37, 37, 37, 37, 6, 6, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4] 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, 58]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000498047301 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498047301 Building ZINC000498058256 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498058256 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/490 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000498058256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498058256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000498058256 none CCS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 9, 7, 7, 7, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/491 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000498058256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498058256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000498058256 none CCS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 10, 10, 9, 9, 9, 4, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000498058256 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 Building ZINC000498058256 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498058256 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 490) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000498058256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498058256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000498058256 none CCS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 9, 7, 7, 7, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 491) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000498058256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498058256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000498058256 none CCS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 10, 10, 9, 9, 9, 4, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000498058256 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498058256 Building ZINC000498099194 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498099194 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/492 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/492' -> `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)Nc1ccccc1S(=O)(=O)N1CCOCC1) `ZINC000498099194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498099194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498099194 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 6, 9, 9, 7, 9, 9, 9, 24, 24, 33, 37, 37, 37, 37, 37, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 6, 9, 9, 9, 9, 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: 134 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/493 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/493' -> `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)Nc1ccccc1S(=O)(=O)N1CCOCC1) `ZINC000498099194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498099194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498099194 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 9, 9, 7, 9, 9, 9, 23, 23, 32, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 6, 9, 9, 7, 9, 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]) total number of confs: 118 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000498099194 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 Building ZINC000498099194 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498099194 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 492) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1S(=O)(=O)N1CCOCC1) `ZINC000498099194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498099194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498099194 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 6, 9, 9, 7, 9, 9, 9, 24, 24, 33, 37, 37, 37, 37, 37, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 6, 9, 9, 9, 9, 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: 134 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 493) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1S(=O)(=O)N1CCOCC1) `ZINC000498099194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498099194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498099194 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1S(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 9, 9, 7, 9, 9, 9, 23, 23, 32, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 6, 9, 9, 7, 9, 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]) total number of confs: 118 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000498099194 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000498099194 Building ZINC000499223311 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499223311 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/494 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C) `ZINC000499223311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499223311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000499223311 none Cc1c(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 20, 8, 8, 4, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/495 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C) `ZINC000499223311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499223311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000499223311 none Cc1c(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 20, 8, 8, 4, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499223311 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 Building ZINC000499223311 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499223311 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 494) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1c(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C) `ZINC000499223311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499223311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000499223311 none Cc1c(NC(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 20, 8, 8, 4, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 495) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1c(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C) `ZINC000499223311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499223311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000499223311 none Cc1c(NC(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)c(=O)n(c2ccccc2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 20, 8, 8, 4, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499223311 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499223311 Building ZINC000499227191 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499227191 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/496 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1) `ZINC000499227191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499227191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000499227191 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 3, 8, 8, 8, 8, 13, 24, 24, 17, 24, 24, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 13, 13, 24, 24, 24, 24, 24, 24, 3] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/497 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1) `ZINC000499227191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499227191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000499227191 none Cn1cc([C@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 9, 9, 9, 9, 9, 2, 6, 6, 6, 6, 11, 22, 22, 15, 22, 22, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 11, 11, 22, 22, 22, 22, 22, 18, 2] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 116 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499227191 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 Building ZINC000499227191 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499227191 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 496) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1) `ZINC000499227191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499227191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000499227191 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 3, 8, 8, 8, 8, 13, 24, 24, 17, 24, 24, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 13, 13, 24, 24, 24, 24, 24, 24, 3] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 497) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1) `ZINC000499227191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499227191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000499227191 none Cn1cc([C@]([O-])([SiH3])C(=O)N(CCC2=CCCCC2)c2c(N)n(Cc3ccccc3)c(=O)nc2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 9, 9, 9, 9, 9, 2, 6, 6, 6, 6, 11, 22, 22, 15, 22, 22, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 11, 11, 22, 22, 22, 22, 22, 18, 2] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 116 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499227191 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499227191 Building ZINC000499233100 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499233100 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/498 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1) `ZINC000499233100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499233100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000499233100 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 14, 14, 14, 15, 15, 15, 15, 15, 4, 4, 4, 4, 16, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 2, 4, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 20, 20, 19, 20, 20, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/499 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1) `ZINC000499233100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499233100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000499233100 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 15, 15, 15, 17, 17, 17, 17, 16, 4, 5, 5, 5, 16, 21, 21, 18, 21, 21, 5, 5, 5, 5, 5, 5, 2, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499233100 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 Building ZINC000499233100 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499233100 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 498) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1) `ZINC000499233100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499233100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000499233100 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 14, 14, 14, 15, 15, 15, 15, 15, 4, 4, 4, 4, 16, 20, 20, 18, 20, 20, 5, 5, 5, 5, 5, 5, 2, 4, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 20, 20, 19, 20, 20, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 499) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1) `ZINC000499233100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499233100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000499233100 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 15, 15, 15, 17, 17, 17, 17, 16, 4, 5, 5, 5, 16, 21, 21, 18, 21, 21, 5, 5, 5, 5, 5, 5, 2, 5, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499233100 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499233100 Building ZINC000499254273 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499254273 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/500 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1) `ZINC000499254273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499254273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000499254273 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 24, 24, 24, 32, 32, 32, 32, 28, 8, 8, 8, 12, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 4, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/501 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1) `ZINC000499254273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499254273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000499254273 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 24, 24, 24, 31, 31, 31, 31, 28, 8, 8, 8, 12, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 4, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499254273 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 Building ZINC000499254273 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499254273 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 500) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1) `ZINC000499254273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499254273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000499254273 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 24, 24, 24, 32, 32, 32, 32, 28, 8, 8, 8, 12, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 4, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 501) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1) `ZINC000499254273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499254273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000499254273 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCCCC3)ccc2N2CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 24, 24, 24, 31, 31, 31, 31, 28, 8, 8, 8, 12, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 4, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499254273 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499254273 Building ZINC000499256204 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499256204 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/502 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C) `ZINC000499256204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499256204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000499256204 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 8, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 31, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 14, 14, 14, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/503 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C) `ZINC000499256204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499256204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000499256204 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 8, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 30, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 14, 14, 14, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499256204 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 Building ZINC000499256204 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499256204 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 502) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C) `ZINC000499256204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499256204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000499256204 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 8, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 31, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 14, 14, 14, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 503) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C) `ZINC000499256204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499256204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000499256204 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)ccc1Sc1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 8, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 6, 14, 14, 14, 30, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 14, 14, 14, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000499256204 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000499256204 Building ZINC000500272254 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500272254 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/504 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000500272254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500272254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000500272254 none COCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/505 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000500272254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500272254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000500272254 none COCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 8, 8, 8, 8, 8, 8, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 5, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 12, 12, 12, 12, 12, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000500272254 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 Building ZINC000500272254 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000500272254 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 504) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000500272254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000500272254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000500272254 none COCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 505) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000500272254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000500272254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000500272254 none COCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 8, 8, 8, 8, 8, 8, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 5, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 12, 12, 12, 12, 12, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000500272254 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000500272254 Building ZINC000501409784 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000501409784 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/506 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/506' -> `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)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 40, 40, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 40, 40, 40, 40, 50, 50, 50, 50, 40, 40, 40, 40, 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/507 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/507' -> `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)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 30, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 43, 43, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 18, 18, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/508 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/508' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 43, 43, 43, 43, 50, 50, 49, 44, 50, 50, 43, 43, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/509 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/509' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 20, 20, 20, 20, 30, 45, 45, 45, 45, 50, 50, 45, 45, 50, 50, 45, 45, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 20, 20, 45, 45, 45, 45, 50, 50, 50, 50, 45, 45, 45, 45, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000501409784 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 Building ZINC000501409784 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000501409784 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 506) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 40, 40, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 40, 40, 40, 40, 50, 50, 50, 50, 40, 40, 40, 40, 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 507) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 30, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 43, 43, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 18, 18, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 508) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 43, 43, 43, 43, 50, 50, 49, 44, 50, 50, 43, 43, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 509) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 20, 20, 20, 20, 30, 45, 45, 45, 45, 50, 50, 45, 45, 50, 50, 45, 45, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 20, 20, 45, 45, 45, 45, 50, 50, 50, 50, 45, 45, 45, 45, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000501409784 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 Building ZINC000501409784 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000501409784 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 506) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 40, 40, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 40, 40, 40, 40, 50, 50, 50, 50, 40, 40, 40, 40, 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 507) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 30, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 43, 43, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 18, 18, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 508) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 43, 43, 43, 43, 50, 50, 49, 44, 50, 50, 43, 43, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 509) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 20, 20, 20, 20, 30, 45, 45, 45, 45, 50, 50, 45, 45, 50, 50, 45, 45, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 20, 20, 45, 45, 45, 45, 50, 50, 50, 50, 45, 45, 45, 45, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000501409784 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 Building ZINC000501409784 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000501409784 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 506) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 40, 40, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 40, 40, 40, 40, 50, 50, 50, 50, 40, 40, 40, 40, 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 507) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 30, 43, 43, 43, 43, 50, 50, 50, 50, 50, 50, 43, 43, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 18, 18, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 508) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 17, 17, 17, 17, 28, 43, 43, 43, 43, 50, 50, 49, 44, 50, 50, 43, 43, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 17, 17, 43, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 509) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1) `ZINC000501409784.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000501409784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000501409784 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc([N@]2CC[N@@](c3ccc(F)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 20, 20, 20, 20, 30, 45, 45, 45, 45, 50, 50, 45, 45, 50, 50, 45, 45, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 20, 20, 45, 45, 45, 45, 50, 50, 50, 50, 45, 45, 45, 45, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000501409784 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501409784 Building ZINC000501896981 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000501896981 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/510 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/510' -> `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(S(=O)(=O)N2CCN(C)CC2)c1) `ZINC000501896981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501896981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000501896981 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCN(C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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'] 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, 14, 11, 11, 8, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 3, 11, 11, 31, 31, 33, 43, 43, 43, 43, 43, 39, 11, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 11, 11, 3, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/511 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/511' -> `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(S(=O)(=O)N2CCN(C)CC2)c1) `ZINC000501896981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501896981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000501896981 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCN(C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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'] 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, 14, 11, 11, 8, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 9, 11, 11, 31, 31, 33, 43, 43, 43, 43, 43, 36, 11, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 11, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000501896981 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 Building ZINC000501896981 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000501896981 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 510) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCN(C)CC2)c1) `ZINC000501896981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000501896981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000501896981 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCN(C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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'] 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, 14, 11, 11, 8, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 3, 11, 11, 31, 31, 33, 43, 43, 43, 43, 43, 39, 11, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 11, 11, 3, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 511) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCN(C)CC2)c1) `ZINC000501896981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000501896981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000501896981 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(S(=O)(=O)N2CCN(C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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'] 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, 14, 11, 11, 8, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 9, 11, 11, 31, 31, 33, 43, 43, 43, 43, 43, 36, 11, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 11, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000501896981 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000501896981 Building ZINC000502031416 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000502031416 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/512 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1) `ZINC000502031416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502031416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000502031416 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 11, 23, 23, 23, 23, 45, 45, 45, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/513 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1) `ZINC000502031416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502031416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000502031416 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 10, 27, 27, 27, 27, 47, 47, 47, 50, 50, 50, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27, 27, 27, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502031416 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 Building ZINC000502031416 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000502031416 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 512) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1) `ZINC000502031416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502031416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000502031416 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 11, 23, 23, 23, 23, 45, 45, 45, 50, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 513) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1) `ZINC000502031416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502031416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000502031416 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 10, 27, 27, 27, 27, 47, 47, 47, 50, 50, 50, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27, 27, 27, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502031416 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502031416 Building ZINC000502491495 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000502491495 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/514 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/514' -> `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(=O)N1CCN(Cc2ccccc2)CC1) `ZINC000502491495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502491495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000502491495 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 9, 9, 17, 17, 17, 17, 29, 41, 41, 29, 41, 41, 17, 17, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 17, 17, 17, 17, 29, 29, 41, 41, 29, 41, 41, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/515 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/515' -> `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(=O)N1CCN(Cc2ccccc2)CC1) `ZINC000502491495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502491495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000502491495 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 16, 16, 16, 16, 29, 39, 39, 29, 39, 39, 16, 16, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 4, 4, 16, 16, 16, 16, 29, 29, 39, 39, 29, 39, 39, 16, 16, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502491495 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 Building ZINC000502491495 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000502491495 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 514) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(Cc2ccccc2)CC1) `ZINC000502491495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502491495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000502491495 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 9, 9, 17, 17, 17, 17, 29, 41, 41, 29, 41, 41, 17, 17, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 17, 17, 17, 17, 29, 29, 41, 41, 29, 41, 41, 17, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 515) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(Cc2ccccc2)CC1) `ZINC000502491495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502491495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000502491495 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 16, 16, 16, 16, 29, 39, 39, 29, 39, 39, 16, 16, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 4, 4, 16, 16, 16, 16, 29, 29, 39, 39, 29, 39, 39, 16, 16, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502491495 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502491495 Building ZINC000502853204 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000502853204 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/516 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/516' -> `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)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1) `ZINC000502853204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502853204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000502853204 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 9, 9, 9, 9, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/517 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/517' -> `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)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1) `ZINC000502853204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502853204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000502853204 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 7, 7, 7, 7, 18, 18, 18, 34, 34, 34, 34, 34, 34, 34, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502853204 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 Building ZINC000502853204 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000502853204 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 516) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1) `ZINC000502853204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502853204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000502853204 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 9, 9, 9, 9, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 517) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1) `ZINC000502853204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502853204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000502853204 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)N(C)C2CCCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 7, 7, 7, 7, 18, 18, 18, 34, 34, 34, 34, 34, 34, 34, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502853204 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502853204 Building ZINC000502864848 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000502864848 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/518 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 42, 42, 42, 42, 42, 42, 42, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/519 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 11, 11, 11, 27, 27, 45, 45, 45, 45, 45, 45, 45, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/520 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/520' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 8, 19, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/521 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/521' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 8, 20, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502864848 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 Building ZINC000502864848 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000502864848 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 518) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 42, 42, 42, 42, 42, 42, 42, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 519) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 11, 11, 11, 27, 27, 45, 45, 45, 45, 45, 45, 45, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 520) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 8, 19, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 521) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 8, 20, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502864848 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 Building ZINC000502864848 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000502864848 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 518) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 42, 42, 42, 42, 42, 42, 42, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 519) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 11, 11, 11, 27, 27, 45, 45, 45, 45, 45, 45, 45, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 520) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 8, 19, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 521) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 8, 20, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502864848 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 Building ZINC000502864848 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000502864848 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 518) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 42, 42, 42, 42, 42, 42, 42, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 4] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 519) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000502864848 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1cccc(NC(=O)C(=O)c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 11, 11, 11, 27, 27, 45, 45, 45, 45, 45, 45, 45, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 520) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 8, 19, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 521) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000502864848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000502864848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000502864848 none CCN(C(=O)C(=O)c1c(C)nn(C)c1C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 11, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 8, 20, 24, 24, 29, 29, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000502864848 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000502864848 Building ZINC000504698340 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000504698340 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/522 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1) `ZINC000504698340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000504698340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000504698340 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 9, 9, 9, 34, 34, 34, 34, 34, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 34, 34, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/523 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1) `ZINC000504698340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000504698340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000504698340 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 2, 2, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 9, 9, 9, 33, 33, 33, 33, 33, 5, 5, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 33, 33, 5, 5, 5, 5, 2] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000504698340 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 Building ZINC000504698340 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000504698340 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 522) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1) `ZINC000504698340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000504698340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000504698340 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 9, 9, 9, 34, 34, 34, 34, 34, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 34, 34, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 523) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1) `ZINC000504698340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000504698340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000504698340 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3ccc(Cl)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 2, 2, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 9, 9, 9, 33, 33, 33, 33, 33, 5, 5, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 33, 33, 5, 5, 5, 5, 2] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000504698340 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000504698340 Building ZINC000505990131 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000505990131 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/524 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000505990131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000505990131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000505990131 none CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 23, 4, 4, 4, 2, 4, 4, 12, 12, 12, 15, 15, 15, 15, 13, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 23, 23, 23, 23, 23, 23, 23, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 4, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 60, 61, 62]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/525 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000505990131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000505990131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000505990131 none CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 22, 4, 4, 4, 4, 4, 4, 13, 13, 13, 16, 16, 16, 16, 13, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 22, 22, 22, 22, 22, 22, 22, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 4, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 60, 61, 62]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000505990131 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 Building ZINC000505990131 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000505990131 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 524) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000505990131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000505990131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000505990131 none CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 23, 4, 4, 4, 2, 4, 4, 12, 12, 12, 15, 15, 15, 15, 13, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 23, 23, 23, 23, 23, 23, 23, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 4, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 60, 61, 62]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 525) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000505990131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000505990131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000505990131 none CC(C)Oc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 22, 4, 4, 4, 4, 4, 4, 13, 13, 13, 16, 16, 16, 16, 13, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 22, 22, 22, 22, 22, 22, 22, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 4, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 60, 61, 62]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000505990131 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000505990131 Building ZINC000506218404 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506218404 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/526 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O) `ZINC000506218404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506218404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000506218404 none CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 13, 10, 5, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 6, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 13, 13, 10, 10, 5, 5, 4, 4, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 15] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/527 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O) `ZINC000506218404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506218404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000506218404 none CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 13, 10, 5, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 6, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 13, 13, 10, 10, 5, 5, 4, 4, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 15] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506218404 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 Building ZINC000506218404 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506218404 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 526) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O) `ZINC000506218404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506218404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000506218404 none CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 13, 10, 5, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 6, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 13, 13, 10, 10, 5, 5, 4, 4, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 15] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 527) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O) `ZINC000506218404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506218404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000506218404 none CCCCn1c(N)c(N(Cc2ccco2)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 13, 10, 5, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 6, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 13, 13, 10, 10, 5, 5, 4, 4, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 15] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506218404 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506218404 Building ZINC000506219930 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506219930 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/528 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000506219930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506219930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000506219930 none CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 6, 10, 10, 10, 10, 16, 35, 35, 19, 35, 35, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 10, 10, 16, 16, 35, 35, 35, 35, 35, 30] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 205 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/529 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000506219930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506219930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000506219930 none CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 5, 8, 8, 8, 8, 17, 33, 33, 18, 33, 33, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 17, 17, 33, 33, 33, 33, 33, 24] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 183 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506219930 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 Building ZINC000506219930 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506219930 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 528) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000506219930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506219930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000506219930 none CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 6, 10, 10, 10, 10, 16, 35, 35, 19, 35, 35, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 10, 10, 16, 16, 35, 35, 35, 35, 35, 30] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 205 number of broken/clashed sets: 130 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 529) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000506219930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506219930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000506219930 none CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 5, 8, 8, 8, 8, 17, 33, 33, 18, 33, 33, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 17, 17, 33, 33, 33, 33, 33, 24] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 183 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506219930 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506219930 Building ZINC000506230119 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506230119 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/530 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cn1) `ZINC000506230119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506230119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000506230119 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 22, 22, 26, 29, 29, 29, 29, 26, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 5, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/531 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cn1) `ZINC000506230119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506230119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000506230119 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 22, 22, 27, 30, 30, 30, 30, 27, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506230119 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 Building ZINC000506230119 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506230119 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 530) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cn1) `ZINC000506230119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506230119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000506230119 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 22, 22, 26, 29, 29, 29, 29, 26, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 5, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 531) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cn1) `ZINC000506230119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506230119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000506230119 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 22, 22, 27, 30, 30, 30, 30, 27, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506230119 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506230119 Building ZINC000506233369 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506233369 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/532 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000506233369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506233369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC000506233369 none CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 8, 7, 7, 6, 7, 7, 21, 21, 25, 34, 34, 34, 34, 27, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/533 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000506233369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506233369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC000506233369 none CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 8, 7, 7, 5, 7, 7, 21, 21, 24, 28, 28, 28, 28, 24, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 10, 10, 10, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506233369 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 Building ZINC000506233369 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506233369 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 532) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000506233369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506233369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC000506233369 none CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 8, 7, 7, 6, 7, 7, 21, 21, 25, 34, 34, 34, 34, 27, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 533) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000506233369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506233369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC000506233369 none CCN(CC)c1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 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, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 8, 7, 7, 5, 7, 7, 21, 21, 24, 28, 28, 28, 28, 24, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 10, 10, 10, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506233369 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233369 Building ZINC000506233440 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506233440 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/534 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)c2)cn1) `ZINC000506233440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506233440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000506233440 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 24, 24, 32, 32, 32, 32, 32, 32, 10, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/535 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)c2)cn1) `ZINC000506233440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506233440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000506233440 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 10, 2, 8, 10, 10, 25, 25, 33, 33, 33, 33, 33, 33, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506233440 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 Building ZINC000506233440 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506233440 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 534) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)c2)cn1) `ZINC000506233440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506233440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000506233440 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 24, 24, 32, 32, 32, 32, 32, 32, 10, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 535) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)c2)cn1) `ZINC000506233440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506233440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000506233440 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)N3CCOCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 10, 10, 2, 8, 10, 10, 25, 25, 33, 33, 33, 33, 33, 33, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506233440 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506233440 Building ZINC000506235791 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506235791 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/536 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000506235791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506235791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000506235791 none CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 22, 5, 14, 14, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/537 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000506235791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506235791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000506235791 none CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 21, 5, 14, 14, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 5, 22, 22, 22, 22, 22, 21, 21, 21, 21, 21, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506235791 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 Building ZINC000506235791 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506235791 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 536) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000506235791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506235791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000506235791 none CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 22, 5, 14, 14, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 537) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000506235791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506235791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC000506235791 none CCN(CC)S(=O)(=O)c1ccc(N2CCOCC2)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 21, 5, 14, 14, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 5, 22, 22, 22, 22, 22, 21, 21, 21, 21, 21, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506235791 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506235791 Building ZINC000506539881 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506539881 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/538 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/538' -> `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)Nc1ncn(CC(=O)NCc2ccccc2)n1) `ZINC000506539881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506539881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000506539881 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(CC(=O)NCc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 17, 17, 17, 46, 46, 46, 46, 46, 46, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 13, 13, 17, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/539 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/539' -> `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)Nc1ncn(CC(=O)NCc2ccccc2)n1) `ZINC000506539881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506539881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000506539881 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(CC(=O)NCc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 10, 15, 15, 15, 49, 50, 50, 49, 50, 50, 4, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 4, 10, 10, 15, 49, 49, 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506539881 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 Building ZINC000506539881 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000506539881 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 538) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(CC(=O)NCc2ccccc2)n1) `ZINC000506539881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000506539881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000506539881 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncn(CC(=O)NCc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 17, 17, 17, 46, 46, 46, 46, 46, 46, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 13, 13, 17, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 539) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(CC(=O)NCc2ccccc2)n1) `ZINC000506539881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000506539881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000506539881 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncn(CC(=O)NCc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 10, 15, 15, 15, 49, 50, 50, 49, 50, 50, 4, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 4, 10, 10, 15, 49, 49, 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000506539881 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000506539881 Building ZINC000508509633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508509633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/540 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1) `ZINC000508509633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508509633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000508509633 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 11, 26, 26, 26, 26, 29, 29, 26, 24, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 26, 26, 26, 26, 29, 29, 29, 26, 26, 26, 26] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/541 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1) `ZINC000508509633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508509633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000508509633 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 5, 12, 28, 28, 28, 28, 30, 30, 28, 26, 5, 6, 6, 6, 5, 5, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 28, 28, 28, 28, 30, 30, 30, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000508509633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 Building ZINC000508509633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508509633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 540) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1) `ZINC000508509633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508509633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000508509633 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 11, 26, 26, 26, 26, 29, 29, 26, 24, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 26, 26, 26, 26, 29, 29, 29, 26, 26, 26, 26] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 541) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1) `ZINC000508509633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508509633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000508509633 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(N2CCN(C(C)=O)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 5, 5, 8, 1, 5, 11, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 5, 12, 28, 28, 28, 28, 30, 30, 28, 26, 5, 6, 6, 6, 5, 5, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 28, 28, 28, 28, 30, 30, 30, 28, 28, 28, 28] 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]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000508509633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508509633 Building ZINC000508913334 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508913334 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/542 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1) `ZINC000508913334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508913334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000508913334 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 14, 14, 14, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 2, 4, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 19, 19, 19, 19, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/543 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1) `ZINC000508913334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508913334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000508913334 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 15, 15, 15, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 2, 5, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 20, 20, 20, 20, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000508913334 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 Building ZINC000508913334 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508913334 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 542) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1) `ZINC000508913334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508913334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000508913334 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 14, 14, 14, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 2, 4, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 19, 19, 19, 19, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 543) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1) `ZINC000508913334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508913334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000508913334 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2Oc2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 15, 15, 15, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 20, 20, 20, 20, 20, 20, 5, 5, 5, 5, 5, 5, 2, 5, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 20, 20, 20, 20, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/194367/xbs-8058088.45/working/building/ZINC000508913334 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000508913334 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000508913334 Building ZINC000511654782 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511654782 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/544 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O) `ZINC000511654782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511654782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000511654782 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 5, 11, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 14, 14, 14] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 10, 43] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/545 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O) `ZINC000511654782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511654782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000511654782 none CCN(CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 5, 11, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 14, 14, 14] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 10, 43] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511654782 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 Building ZINC000511654782 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511654782 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 544) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O) `ZINC000511654782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511654782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000511654782 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 5, 11, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 14, 14, 14] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 10, 43] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 545) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O) `ZINC000511654782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511654782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000511654782 none CCN(CCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 5, 11, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6, 6, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 14, 14, 14] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 10, 43] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511654782 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511654782 Building ZINC000511742079 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511742079 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/546 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1) `ZINC000511742079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511742079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000511742079 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 28, 28, 28, 28, 32, 32, 29, 32, 32, 28, 28, 28, 28, 10, 10, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 10, 10, 10, 10, 28, 32, 32, 29, 32, 32, 10, 10, 10, 10, 4] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/547 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1) `ZINC000511742079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511742079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000511742079 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 3, 3, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 28, 28, 28, 28, 29, 29, 28, 29, 29, 28, 28, 28, 28, 8, 8, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 28, 29, 29, 28, 29, 29, 8, 8, 8, 8, 3] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511742079 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 Building ZINC000511742079 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511742079 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 546) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1) `ZINC000511742079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511742079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000511742079 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 28, 28, 28, 28, 32, 32, 29, 32, 32, 28, 28, 28, 28, 10, 10, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 10, 10, 10, 10, 28, 32, 32, 29, 32, 32, 10, 10, 10, 10, 4] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 547) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1) `ZINC000511742079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511742079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000511742079 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3cnn(c4ccccc4)c(=O)c3Cl)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'Cl', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 3, 3, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 28, 28, 28, 28, 29, 29, 28, 29, 29, 28, 28, 28, 28, 8, 8, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 28, 29, 29, 28, 29, 29, 8, 8, 8, 8, 3] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511742079 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511742079 Building ZINC000511775495 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511775495 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/548 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1) `ZINC000511775495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511775495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511775495 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 18, 18, 18, 36, 36, 36, 36, 36, 11, 11, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 11, 36, 36, 11, 11, 11, 11, 2] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/549 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1) `ZINC000511775495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511775495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511775495 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 15, 15, 15, 32, 32, 32, 32, 32, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 32, 32, 7, 7, 7, 7, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511775495 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 Building ZINC000511775495 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511775495 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 548) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1) `ZINC000511775495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511775495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511775495 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 18, 18, 18, 36, 36, 36, 36, 36, 11, 11, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 11, 36, 36, 11, 11, 11, 11, 2] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 549) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1) `ZINC000511775495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511775495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000511775495 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)s3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 15, 15, 15, 32, 32, 32, 32, 32, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 32, 32, 7, 7, 7, 7, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511775495 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511775495 Building ZINC000511816548 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511816548 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/550 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1) `ZINC000511816548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511816548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000511816548 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 5, 8, 15, 15, 15, 15, 26, 26, 26, 32, 32, 31, 31, 32, 32, 15, 15, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 15, 15, 15, 32, 32, 32, 32, 15, 15, 15, 15, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/551 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1) `ZINC000511816548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511816548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000511816548 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 26, 26, 26, 32, 32, 30, 30, 32, 32, 13, 13, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 13, 13, 13, 13, 32, 32, 32, 32, 13, 13, 13, 13, 5] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511816548 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 Building ZINC000511816548 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000511816548 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 550) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1) `ZINC000511816548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000511816548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000511816548 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 5, 8, 15, 15, 15, 15, 26, 26, 26, 32, 32, 31, 31, 32, 32, 15, 15, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 15, 15, 15, 32, 32, 32, 32, 15, 15, 15, 15, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 551) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1) `ZINC000511816548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000511816548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000511816548 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(Br)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 5, 5, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 26, 26, 26, 32, 32, 30, 30, 32, 32, 13, 13, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 13, 13, 13, 13, 32, 32, 32, 32, 13, 13, 13, 13, 5] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000511816548 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000511816548 Building ZINC000512204669 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512204669 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/552 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC) `ZINC000512204669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512204669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC000512204669 none CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', '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', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 4, 4, 12, 12, 12, 32, 36, 29, 29, 29, 29, 29, 12, 12, 4, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 4, 12, 36, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/553 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC) `ZINC000512204669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512204669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC000512204669 none CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', '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', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 8, 6, 8, 8, 6, 6, 6, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 6, 6, 19, 19, 19, 38, 40, 41, 41, 41, 41, 41, 19, 19, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 6, 6, 19, 40, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000512204669 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 Building ZINC000512204669 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000512204669 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 552) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC) `ZINC000512204669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000512204669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC000512204669 none CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', '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', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 4, 4, 12, 12, 12, 32, 36, 29, 29, 29, 29, 29, 12, 12, 4, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 4, 12, 36, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 553) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC) `ZINC000512204669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000512204669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC000512204669 none CCOc1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', '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', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 8, 6, 8, 8, 6, 6, 6, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 6, 6, 19, 19, 19, 38, 40, 41, 41, 41, 41, 41, 19, 19, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 6, 6, 19, 40, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000512204669 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000512204669 Building ZINC000513178527 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513178527 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/554 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC000513178527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513178527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000513178527 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 14, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 27, 27, 19, 19, 14, 14, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21] 150 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]) total number of confs: 126 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/555 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC000513178527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513178527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000513178527 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 14, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 27, 27, 19, 19, 14, 14, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21] 150 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]) total number of confs: 126 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000513178527 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 Building ZINC000513178527 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000513178527 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 554) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC000513178527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000513178527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000513178527 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 14, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 27, 27, 19, 19, 14, 14, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21] 150 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]) total number of confs: 126 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 555) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC000513178527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000513178527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000513178527 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 19, 14, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 27, 27, 19, 19, 14, 14, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21] 150 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]) total number of confs: 126 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000513178527 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000513178527 Building ZINC000514348251 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514348251 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/556 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000514348251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514348251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000514348251 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 5, 5, 3, 7, 7, 7, 7, 21, 37, 37, 25, 37, 37, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 7, 7, 21, 21, 37, 37, 37, 37, 37, 21] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 171 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/557 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000514348251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514348251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000514348251 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 2, 6, 6, 6, 6, 18, 37, 37, 19, 37, 37, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 6, 6, 18, 18, 37, 37, 36, 37, 37, 18] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 186 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514348251 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 Building ZINC000514348251 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514348251 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 556) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000514348251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514348251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000514348251 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 5, 5, 3, 7, 7, 7, 7, 21, 37, 37, 25, 37, 37, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 7, 7, 21, 21, 37, 37, 37, 37, 37, 21] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 171 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 557) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000514348251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514348251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000514348251 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCC(C)C)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 2, 6, 6, 6, 6, 18, 37, 37, 19, 37, 37, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 6, 6, 18, 18, 37, 37, 36, 37, 37, 18] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 186 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514348251 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514348251 Building ZINC000514484442 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514484442 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/558 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cc1) `ZINC000514484442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514484442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000514484442 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 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, 6, 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, 7, 7] 0 hydrogens 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, 10, 10, 10, 38, 38, 47, 50, 50, 50, 50, 48, 6, 10, 10, 10, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 4, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/559 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cc1) `ZINC000514484442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514484442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000514484442 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 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, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 38, 38, 46, 49, 49, 49, 49, 46, 7, 10, 10, 10, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 4, 10, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514484442 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 Building ZINC000514484442 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514484442 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 558) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cc1) `ZINC000514484442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514484442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000514484442 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 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, 6, 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, 7, 7] 0 hydrogens 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, 10, 10, 10, 38, 38, 47, 50, 50, 50, 50, 48, 6, 10, 10, 10, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 4, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 559) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)cc1) `ZINC000514484442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514484442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000514484442 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2N2CCCC2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 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, 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, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 38, 38, 46, 49, 49, 49, 49, 46, 7, 10, 10, 10, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 4, 10, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514484442 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514484442 Building ZINC000514489854 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514489854 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/560 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/560' -> `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(F)c(S(=O)(=O)N2CCOCC2)c1) `ZINC000514489854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514489854 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 14, 14, 4, 4, 14, 14, 39, 39, 43, 46, 46, 46, 46, 44, 14, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/561 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/561' -> `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(F)c(S(=O)(=O)N2CCOCC2)c1) `ZINC000514489854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514489854 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 8, 11, 11, 36, 36, 39, 42, 42, 42, 42, 39, 11, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 3, 2, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 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]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514489854 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 Building ZINC000514489854 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514489854 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 560) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(S(=O)(=O)N2CCOCC2)c1) `ZINC000514489854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514489854 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 14, 14, 4, 4, 14, 14, 39, 39, 43, 46, 46, 46, 46, 44, 14, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 14, 14, 46, 46, 46, 46, 46, 46, 46, 46, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 561) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(S(=O)(=O)N2CCOCC2)c1) `ZINC000514489854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514489854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514489854 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(S(=O)(=O)N2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 8, 11, 11, 36, 36, 39, 42, 42, 42, 42, 39, 11, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 3, 2, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 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]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514489854 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514489854 Building ZINC000514899534 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514899534 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/562 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/562' -> `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(S(=O)(=O)N2CCOCC2)cc1) `ZINC000514899534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514899534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514899534 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 4, 5, 22, 22, 25, 40, 40, 40, 40, 28, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 5, 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/563 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/563' -> `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(S(=O)(=O)N2CCOCC2)cc1) `ZINC000514899534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514899534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514899534 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 24, 24, 27, 42, 42, 42, 42, 30, 5, 5, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 5, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514899534 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 Building ZINC000514899534 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000514899534 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 562) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCOCC2)cc1) `ZINC000514899534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000514899534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514899534 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 4, 5, 22, 22, 25, 40, 40, 40, 40, 28, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 5, 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 563) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCOCC2)cc1) `ZINC000514899534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000514899534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000514899534 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(S(=O)(=O)N2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 24, 24, 27, 42, 42, 42, 42, 30, 5, 5, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 5, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000514899534 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000514899534 Building ZINC000515337716 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515337716 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/564 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000515337716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515337716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000515337716 none COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 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: [15, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 11, 26, 26, 14, 26, 26, 6, 6, 6, 6, 6, 15, 15, 15, 9, 9, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 26, 26, 26, 26, 26, 18] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/565 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000515337716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515337716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000515337716 none COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 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: [15, 10, 5, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 26, 26, 13, 26, 26, 6, 6, 6, 6, 6, 15, 15, 15, 10, 10, 5, 5, 4, 4, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 26, 26, 26, 26, 26, 18] 150 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, 58]) total number of confs: 183 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515337716 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 Building ZINC000515337716 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515337716 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 564) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000515337716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515337716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000515337716 none COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 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: [15, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 11, 26, 26, 14, 26, 26, 6, 6, 6, 6, 6, 15, 15, 15, 9, 9, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 26, 26, 26, 26, 26, 18] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 168 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 565) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000515337716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515337716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000515337716 none COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 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: [15, 10, 5, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 26, 26, 13, 26, 26, 6, 6, 6, 6, 6, 15, 15, 15, 10, 10, 5, 5, 4, 4, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 26, 26, 26, 26, 26, 18] 150 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, 58]) total number of confs: 183 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515337716 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515337716 Building ZINC000515421877 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515421877 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/566 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1) `ZINC000515421877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515421877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421877 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 3, 3, 3, 3, 3, 3, 7, 14, 16, 16, 16, 3, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 7, 7, 14, 16, 16, 16, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/567 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1) `ZINC000515421877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515421877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421877 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 9, 13, 15, 15, 15, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 13, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515421877 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 Building ZINC000515421877 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515421877 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 566) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1) `ZINC000515421877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515421877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421877 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 3, 3, 3, 3, 3, 3, 7, 14, 16, 16, 16, 3, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 7, 7, 14, 16, 16, 16, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 567) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1) `ZINC000515421877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515421877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421877 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 9, 13, 15, 15, 15, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 13, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515421877 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421877 Building ZINC000515421878 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515421878 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/568 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1) `ZINC000515421878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515421878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 13, 15, 15, 15, 3, 2, 2, 2, 9, 9, 7, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 13, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/569 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1) `ZINC000515421878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515421878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 14, 15, 15, 15, 3, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515421878 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 Building ZINC000515421878 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515421878 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 568) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1) `ZINC000515421878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515421878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 13, 15, 15, 15, 3, 2, 2, 2, 9, 9, 7, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 13, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 569) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1) `ZINC000515421878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515421878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000515421878 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CNS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 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] dock 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 14, 15, 15, 15, 3, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 14, 15, 15, 15, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515421878 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515421878 Building ZINC000515503442 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515503442 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/570 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/570' -> `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(C(N)=O)CCOCC1) `ZINC000515503442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515503442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000515503442 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C(N)=O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.am', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 6, 6, 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]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/571 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/571' -> `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(C(N)=O)CCOCC1) `ZINC000515503442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515503442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000515503442 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C(N)=O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.am', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515503442 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 Building ZINC000515503442 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515503442 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 570) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C(N)=O)CCOCC1) `ZINC000515503442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515503442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000515503442 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C(N)=O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.am', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 6, 6, 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]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 571) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C(N)=O)CCOCC1) `ZINC000515503442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515503442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000515503442 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C(N)=O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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.am', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515503442 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515503442 Building ZINC000515542750 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515542750 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/572 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2noc(CN3CCN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1) `ZINC000515542750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515542750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000515542750 none COc1ccc(c2noc(CN3CCN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 9, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 33, 41, 41, 41, 41, 41, 41, 41, 9, 9, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 41, 41] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/573 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2noc(CN3CCN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1) `ZINC000515542750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515542750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000515542750 none COc1ccc(c2noc(CN3CCN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 9, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 32, 37, 37, 37, 37, 37, 37, 37, 9, 9, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 37, 37] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515542750 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 Building ZINC000515542750 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515542750 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 572) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(c2noc(CN3CCN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1) `ZINC000515542750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515542750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000515542750 none COc1ccc(c2noc(CN3CCN(C(=O)[C@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 9, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 33, 41, 41, 41, 41, 41, 41, 41, 9, 9, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 41, 41] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 573) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(c2noc(CN3CCN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1) `ZINC000515542750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515542750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000515542750 none COc1ccc(c2noc(CN3CCN(C(=O)[C@@]([O-])([SiH3])c4cnn(C(C)(C)C)c4)CC3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 9, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 32, 37, 37, 37, 37, 37, 37, 37, 9, 9, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 37, 37] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515542750 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515542750 Building ZINC000515819397 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515819397 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/574 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1) `ZINC000515819397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515819397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000515819397 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 30, 32, 34, 35, 35, 35, 35, 36, 36, 35, 36, 36, 35, 35, 4, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 4, 4, 20, 20, 35, 35, 35, 35, 36, 35, 36, 35, 35, 35, 35, 4, 4, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/575 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1) `ZINC000515819397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515819397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000515819397 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 32, 33, 35, 36, 36, 36, 36, 37, 37, 36, 37, 37, 36, 36, 4, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 4, 4, 20, 20, 36, 36, 36, 36, 37, 36, 37, 36, 36, 36, 36, 4, 4, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 108 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515819397 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 Building ZINC000515819397 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000515819397 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 574) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1) `ZINC000515819397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000515819397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000515819397 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 30, 32, 34, 35, 35, 35, 35, 36, 36, 35, 36, 36, 35, 35, 4, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 4, 4, 20, 20, 35, 35, 35, 35, 36, 35, 36, 35, 35, 35, 35, 4, 4, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 575) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1) `ZINC000515819397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000515819397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC000515819397 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(CC(=O)N3CCN(c4ncccn4)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 32, 33, 35, 36, 36, 36, 36, 37, 37, 36, 37, 37, 36, 36, 4, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 4, 4, 20, 20, 36, 36, 36, 36, 37, 36, 37, 36, 36, 36, 36, 4, 4, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 108 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000515819397 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000515819397 Building ZINC000516362994 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516362994 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/576 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000516362994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516362994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000516362994 none COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 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, 7, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 6, 11, 11, 9, 11, 11, 3, 3, 3, 3, 3, 8, 8, 8, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 9] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 82 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/577 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000516362994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516362994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000516362994 none COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 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, 7, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 6, 11, 11, 10, 11, 11, 3, 3, 3, 3, 3, 8, 8, 8, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 9] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 80 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516362994 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 Building ZINC000516362994 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516362994 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 576) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000516362994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516362994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000516362994 none COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 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, 7, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 6, 11, 11, 9, 11, 11, 3, 3, 3, 3, 3, 8, 8, 8, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 9] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 82 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 577) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000516362994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516362994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000516362994 none COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 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, 7, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 6, 11, 11, 10, 11, 11, 3, 3, 3, 3, 3, 8, 8, 8, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 9] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 80 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516362994 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516362994 Building ZINC000516363600 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516363600 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/578 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000516363600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516363600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516363600 none CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 5, 6, 6, 15, 15, 17, 20, 20, 20, 20, 17, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/579 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000516363600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516363600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516363600 none CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 5, 6, 6, 14, 14, 16, 19, 19, 19, 19, 16, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516363600 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 Building ZINC000516363600 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516363600 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 578) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000516363600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516363600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516363600 none CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 5, 6, 6, 15, 15, 17, 20, 20, 20, 20, 17, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 579) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000516363600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516363600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516363600 none CCOc1ccc(S(=O)(=O)N2CCOCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 5, 6, 6, 14, 14, 16, 19, 19, 19, 19, 16, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516363600 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516363600 Building ZINC000516812309 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516812309 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/580 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC000516812309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516812309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000516812309 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 35, 24, 29, 29, 13, 6, 13, 13, 6, 6, 6, 3, 1, 5, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 6, 6, 29, 29, 36, 36, 36, 36, 36, 29, 29, 6, 6, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 29, 29] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/581 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC000516812309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516812309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000516812309 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 19, 28, 28, 10, 6, 10, 10, 6, 6, 6, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 6, 28, 28, 30, 30, 30, 30, 30, 28, 28, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516812309 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 Building ZINC000516812309 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516812309 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 580) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC000516812309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516812309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000516812309 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 35, 24, 29, 29, 13, 6, 13, 13, 6, 6, 6, 3, 1, 5, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 6, 6, 29, 29, 36, 36, 36, 36, 36, 29, 29, 6, 6, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 29, 29] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 581) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1) `ZINC000516812309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516812309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000516812309 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 19, 28, 28, 10, 6, 10, 10, 6, 6, 6, 2, 1, 3, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 6, 6, 28, 28, 30, 30, 30, 30, 30, 28, 28, 6, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516812309 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812309 Building ZINC000516812404 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516812404 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/582 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1) `ZINC000516812404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516812404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516812404 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1 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.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 19, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/583 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1) `ZINC000516812404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516812404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516812404 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1 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.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 26, 26, 26, 26, 26, 26, 20, 19, 17, 16, 16, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516812404 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 Building ZINC000516812404 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000516812404 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 582) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1) `ZINC000516812404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000516812404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516812404 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1 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.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 16, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 19, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 583) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1) `ZINC000516812404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000516812404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC000516812404 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1S(=O)(=O)N1CCOCC1 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.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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 25, 25, 26, 26, 26, 26, 26, 26, 20, 19, 17, 16, 16, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000516812404 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000516812404 Building ZINC000517469736 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517469736 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/584 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/584' -> `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)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)c1) `ZINC000517469736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517469736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000517469736 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 20, 42, 49, 49, 49, 49, 49, 45, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 13, 13, 13, 20, 42, 42, 49, 49, 49, 49, 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, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/585 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/585' -> `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)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)c1) `ZINC000517469736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517469736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000517469736 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 22, 43, 48, 48, 48, 48, 48, 48, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 14, 14, 14, 22, 43, 43, 48, 48, 48, 48, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000517469736 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 Building ZINC000517469736 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000517469736 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 584) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)c1) `ZINC000517469736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000517469736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000517469736 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 20, 42, 49, 49, 49, 49, 49, 45, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 13, 13, 13, 20, 42, 42, 49, 49, 49, 49, 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, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 585) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)c1) `ZINC000517469736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000517469736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000517469736 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(S(=O)(=O)NCc2cccc(F)c2)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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 22, 43, 48, 48, 48, 48, 48, 48, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 14, 14, 14, 22, 43, 43, 48, 48, 48, 48, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000517469736 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000517469736 Building ZINC000518044856 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518044856 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/586 `/scratch/xiaobo/194367/xbs-8058088.45/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)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518044856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044856 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 7, 7, 33, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/587 `/scratch/xiaobo/194367/xbs-8058088.45/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)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518044856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044856 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 8, 16, 40, 41, 41, 41, 40, 41, 41, 41, 41, 41, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 4, 4, 15, 8, 8, 41, 41, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000518044856 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 Building ZINC000518044856 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518044856 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 586) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518044856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044856 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 7, 7, 33, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 587) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518044856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044856 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 8, 16, 40, 41, 41, 41, 40, 41, 41, 41, 41, 41, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 4, 4, 15, 8, 8, 41, 41, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000518044856 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044856 Building ZINC000518044857 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518044857 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/588 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/588' -> `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](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518044857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044857 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 8, 15, 38, 43, 43, 43, 38, 43, 43, 43, 43, 43, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 4, 4, 15, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/589 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/589' -> `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](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518044857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044857 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 12, 12, 12, 14, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 8, 8, 36, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000518044857 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 Building ZINC000518044857 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518044857 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 588) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518044857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044857 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 8, 15, 38, 43, 43, 43, 38, 43, 43, 43, 43, 43, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 4, 4, 15, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 589) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2) `ZINC000518044857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518044857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000518044857 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 12, 12, 12, 14, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 8, 8, 36, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000518044857 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518044857 Building ZINC000518689203 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518689203 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/590 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518689203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518689203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000518689203 none O=C(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 26, 26, 10, 10, 10, 10, 2, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/591 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518689203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518689203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000518689203 none O=C(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 27, 27, 10, 10, 10, 10, 2, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000518689203 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 Building ZINC000518689203 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000518689203 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 590) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518689203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000518689203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000518689203 none O=C(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 26, 26, 10, 10, 10, 10, 2, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 591) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000518689203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000518689203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000518689203 none O=C(N1CCN(S(=O)(=O)c2ccc(F)c(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 27, 27, 10, 10, 10, 10, 2, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000518689203 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000518689203 Building ZINC000519998550 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000519998550 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/592 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1) `ZINC000519998550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000519998550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 3, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/593 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1) `ZINC000519998550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000519998550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000519998550 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 Building ZINC000519998550 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000519998550 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 592) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1) `ZINC000519998550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000519998550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 3, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 593) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1) `ZINC000519998550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000519998550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998550 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000519998550 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998550 Building ZINC000519998551 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000519998551 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/594 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/594' -> `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]1CCCN(S(C)(=O)=O)C1) `ZINC000519998551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000519998551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998551 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 16, 16, 16, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 13, 13, 13, 13, 13, 13, 16, 16, 16, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/595 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/595' -> `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]1CCCN(S(C)(=O)=O)C1) `ZINC000519998551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000519998551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998551 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000519998551 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 Building ZINC000519998551 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000519998551 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 594) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(C)(=O)=O)C1) `ZINC000519998551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000519998551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998551 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 16, 16, 16, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 13, 13, 13, 13, 13, 13, 16, 16, 16, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 595) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(C)(=O)=O)C1) `ZINC000519998551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000519998551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000519998551 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000519998551 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000519998551 Building ZINC000520481305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520481305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/596 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/596' -> `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(C(=O)NCCN2CCOCC2)cc1) `ZINC000520481305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520481305 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCCN2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 2, 3, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 7, 33, 33, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/597 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/597' -> `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(C(=O)NCCN2CCOCC2)cc1) `ZINC000520481305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520481305 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCCN2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 7, 33, 33, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000520481305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 Building ZINC000520481305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000520481305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 596) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCCN2CCOCC2)cc1) `ZINC000520481305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000520481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520481305 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCCN2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 2, 3, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 7, 33, 33, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 597) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCCN2CCOCC2)cc1) `ZINC000520481305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000520481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000520481305 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NCCN2CCOCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 7, 7, 7, 33, 46, 50, 50, 50, 50, 50, 3, 3, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 7, 33, 33, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000520481305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000520481305 Building ZINC000521177190 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521177190 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/598 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/598' -> `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)NCCS(=O)(=O)NC(C)C) `ZINC000521177190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521177190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000521177190 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 7, 7, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 3, 5, 5, 5, 5, 5, 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: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/599 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/599' -> `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)NCCS(=O)(=O)NC(C)C) `ZINC000521177190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521177190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000521177190 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need 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, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 3, 3, 3, 4, 4, 8, 8, 8, 9, 11, 11, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 3, 4, 4, 4, 4, 9, 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: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000521177190 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 Building ZINC000521177190 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521177190 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 598) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)NC(C)C) `ZINC000521177190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521177190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000521177190 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 7, 7, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 3, 5, 5, 5, 5, 5, 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: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 599) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)NC(C)C) `ZINC000521177190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521177190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000521177190 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need 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, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 3, 3, 3, 4, 4, 8, 8, 8, 9, 11, 11, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 3, 4, 4, 4, 4, 9, 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: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000521177190 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521177190 Building ZINC000521771286 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521771286 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/600 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/600' -> `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)N1CCN(CCNC(=O)c2ccccc2F)CC1) `ZINC000521771286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521771286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000521771286 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2ccccc2F)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 5, 5, 5, 10, 13, 34, 34, 34, 35, 35, 34, 35, 35, 35, 5, 5, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 5, 5, 5, 5, 10, 10, 13, 13, 34, 35, 35, 35, 35, 5, 5, 5, 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, 62]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/601 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/601' -> `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)N1CCN(CCNC(=O)c2ccccc2F)CC1) `ZINC000521771286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521771286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000521771286 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2ccccc2F)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 10, 14, 37, 37, 37, 38, 38, 37, 38, 38, 38, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 10, 10, 14, 14, 37, 38, 38, 38, 38, 4, 4, 4, 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, 62]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000521771286 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 Building ZINC000521771286 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000521771286 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 600) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2ccccc2F)CC1) `ZINC000521771286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000521771286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000521771286 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2ccccc2F)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 5, 5, 5, 10, 13, 34, 34, 34, 35, 35, 34, 35, 35, 35, 5, 5, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 5, 5, 5, 5, 10, 10, 13, 13, 34, 35, 35, 35, 35, 5, 5, 5, 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, 62]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 601) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2ccccc2F)CC1) `ZINC000521771286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000521771286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000521771286 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2ccccc2F)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 10, 14, 37, 37, 37, 38, 38, 37, 38, 38, 38, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 10, 10, 14, 14, 37, 38, 38, 38, 38, 4, 4, 4, 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, 62]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000521771286 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000521771286 Building ZINC000522128842 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522128842 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/602 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1) `ZINC000522128842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522128842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000522128842 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 16, 16, 16, 33, 33, 33, 33, 33, 33, 30, 33, 33, 33, 33, 33, 33, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 33, 33, 33, 10, 10, 10, 10, 2] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/603 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1) `ZINC000522128842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522128842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000522128842 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 13, 31, 31, 31, 31, 31, 31, 7, 7, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 31, 31, 31, 7, 7, 7, 7, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000522128842 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 Building ZINC000522128842 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522128842 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 602) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1) `ZINC000522128842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522128842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000522128842 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 16, 16, 16, 33, 33, 33, 33, 33, 33, 30, 33, 33, 33, 33, 33, 33, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 33, 33, 33, 10, 10, 10, 10, 2] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 603) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1) `ZINC000522128842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522128842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000522128842 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cc(C(F)(F)F)cc(C(F)(F)F)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 13, 31, 31, 31, 31, 31, 31, 7, 7, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 31, 31, 31, 7, 7, 7, 7, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000522128842 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522128842 Building ZINC000522677671 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522677671 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/604 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1) `ZINC000522677671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522677671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC000522677671 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3, 3, 3, 3, 3, 3, 2, 4, 4, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/605 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1) `ZINC000522677671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522677671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC000522677671 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 19, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3, 3, 3, 3, 3, 3, 2, 4, 4, 19, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000522677671 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 Building ZINC000522677671 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522677671 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 604) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1) `ZINC000522677671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522677671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC000522677671 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3, 3, 3, 3, 3, 3, 2, 4, 4, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 605) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1) `ZINC000522677671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522677671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC000522677671 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(NS(=O)(=O)c3ccc4c(c3)OCCCO4)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 19, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3, 3, 3, 3, 3, 3, 2, 4, 4, 19, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 3] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000522677671 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522677671 Building ZINC000522728900 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522728900 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/606 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1) `ZINC000522728900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522728900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000522728900 none CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 37, 29, 38, 38, 29, 22, 10, 22, 22, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 4, 5, 10, 38, 38, 42, 42, 42, 42, 42, 38, 38, 29, 10, 2, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 38, 38] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/607 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1) `ZINC000522728900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522728900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000522728900 none CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 36, 29, 37, 37, 29, 22, 10, 22, 22, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 2, 2, 10, 37, 37, 42, 42, 42, 42, 42, 37, 37, 29, 10, 2, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 37, 37] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000522728900 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 Building ZINC000522728900 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000522728900 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 606) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1) `ZINC000522728900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000522728900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000522728900 none CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 37, 29, 38, 38, 29, 22, 10, 22, 22, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 4, 5, 10, 38, 38, 42, 42, 42, 42, 42, 38, 38, 29, 10, 2, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 38, 38] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 607) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1) `ZINC000522728900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000522728900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000522728900 none CCOc1ccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 36, 29, 37, 37, 29, 22, 10, 22, 22, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 2, 2, 10, 37, 37, 42, 42, 42, 42, 42, 37, 37, 29, 10, 2, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 37, 37] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000522728900 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000522728900 Building ZINC000524279161 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524279161 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/608 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000524279161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524279161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC000524279161 none COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 1, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 34, 34, 34, 34, 34, 34, 16, 9, 16, 16, 9, 9, 9, 3, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/609 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000524279161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524279161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC000524279161 none COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 1, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 50, 38, 38, 38, 38, 38, 38, 16, 8, 16, 16, 8, 8, 8, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000524279161 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 Building ZINC000524279161 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524279161 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 608) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000524279161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524279161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC000524279161 none COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 1, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 34, 34, 34, 34, 34, 34, 16, 9, 16, 16, 9, 9, 9, 3, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 34, 34, 34, 34, 34, 34, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 609) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000524279161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524279161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC000524279161 none COC(=O)c1c(C)oc(C)c1S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 1, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 50, 38, 38, 38, 38, 38, 38, 16, 8, 16, 16, 8, 8, 8, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000524279161 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524279161 Building ZINC000524567113 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524567113 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/610 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1) `ZINC000524567113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524567113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC000524567113 none CCN1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 27, 16, 27, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 32, 32, 42, 42, 42, 42, 42, 32, 32, 32, 32, 16, 16, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 32, 32, 32, 32] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 171 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/611 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1) `ZINC000524567113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524567113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC000524567113 none CCN1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 21, 10, 21, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 33, 33, 37, 37, 37, 37, 37, 33, 33, 33, 33, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 33, 33, 33, 33] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000524567113 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 Building ZINC000524567113 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524567113 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 610) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1) `ZINC000524567113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524567113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC000524567113 none CCN1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 27, 16, 27, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 32, 32, 42, 42, 42, 42, 42, 32, 32, 32, 32, 16, 16, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 32, 32, 32, 32] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 171 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 611) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1) `ZINC000524567113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524567113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC000524567113 none CCN1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 21, 10, 21, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 33, 33, 37, 37, 37, 37, 37, 33, 33, 33, 33, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 33, 33, 33, 33] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 135 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000524567113 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524567113 Building ZINC000524701176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524701176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/612 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/612' -> `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(=O)NCCC(N)=O)ccc1F) `ZINC000524701176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524701176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000524701176 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(=O)NCCC(N)=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', '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'] 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, 11, 8, 5, 5, 1, 8, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 8, 8, 8, 22, 31, 44, 44, 4, 4, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 4, 8, 22, 22, 31, 31, 44, 44, 4, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/613 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/613' -> `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(=O)NCCC(N)=O)ccc1F) `ZINC000524701176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524701176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000524701176 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(=O)NCCC(N)=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', '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'] 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, 11, 8, 5, 5, 1, 8, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 22, 32, 45, 45, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 8, 22, 22, 32, 32, 45, 45, 4, 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]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000524701176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 Building ZINC000524701176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524701176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 612) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(=O)NCCC(N)=O)ccc1F) `ZINC000524701176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524701176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000524701176 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(=O)NCCC(N)=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', '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'] 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, 11, 8, 5, 5, 1, 8, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 8, 8, 8, 22, 31, 44, 44, 4, 4, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 4, 8, 22, 22, 31, 31, 44, 44, 4, 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]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 613) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(=O)NCCC(N)=O)ccc1F) `ZINC000524701176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524701176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000524701176 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(=O)NCCC(N)=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', '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'] 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, 11, 8, 5, 5, 1, 8, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 22, 32, 45, 45, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 8, 22, 22, 32, 32, 45, 45, 4, 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]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000524701176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000524701176 Building ZINC000552544981 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552544981 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/614 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552544981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544981 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 8, 8, 11, 11, 11, 33, 35, 35, 34, 35, 35, 8, 9, 9, 9, 9, 9, 5, 5, 2, 2, 5, 5, 5, 5, 5, 2, 5, 5, 5, 5, 11, 33, 33, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 5, 5, 5, 5, 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, 62]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/615 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552544981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544981 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 9, 9, 12, 12, 12, 36, 37, 37, 36, 37, 37, 9, 10, 10, 10, 10, 10, 6, 6, 2, 2, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 12, 36, 36, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 6, 6, 6, 6, 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, 62]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000552544981 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 Building ZINC000552544981 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552544981 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 614) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552544981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544981 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 8, 8, 11, 11, 11, 33, 35, 35, 34, 35, 35, 8, 9, 9, 9, 9, 9, 5, 5, 2, 2, 5, 5, 5, 5, 5, 2, 5, 5, 5, 5, 11, 33, 33, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 5, 5, 5, 5, 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, 62]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 615) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552544981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544981 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 9, 9, 12, 12, 12, 36, 37, 37, 36, 37, 37, 9, 10, 10, 10, 10, 10, 6, 6, 2, 2, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 12, 36, 36, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 6, 6, 6, 6, 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, 62]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000552544981 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544981 Building ZINC000552544982 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552544982 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/616 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552544982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544982 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 7, 10, 10, 10, 32, 35, 35, 34, 35, 35, 7, 7, 7, 7, 7, 7, 4, 4, 2, 2, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 10, 32, 32, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 4, 4, 4, 4, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/617 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552544982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544982 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 7, 9, 9, 9, 30, 34, 34, 33, 34, 34, 7, 7, 7, 7, 7, 7, 4, 4, 3, 3, 7, 7, 7, 7, 7, 3, 4, 4, 4, 4, 9, 30, 30, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 4, 4, 4, 4, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000552544982 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 Building ZINC000552544982 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552544982 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 616) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552544982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544982 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 7, 10, 10, 10, 32, 35, 35, 34, 35, 35, 7, 7, 7, 7, 7, 7, 4, 4, 2, 2, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 10, 32, 32, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 4, 4, 4, 4, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 617) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1) `ZINC000552544982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552544982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000552544982 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](C(=O)NCc3ccccc3)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 7, 9, 9, 9, 30, 34, 34, 33, 34, 34, 7, 7, 7, 7, 7, 7, 4, 4, 3, 3, 7, 7, 7, 7, 7, 3, 4, 4, 4, 4, 9, 30, 30, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 4, 4, 4, 4, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000552544982 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000552544982 Building ZINC000566512750 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000566512750 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/618 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000566512750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566512750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000566512750 none CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 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, 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: [23, 23, 23, 23, 15, 5, 15, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 23, 23, 23, 23, 26, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 5, 5, 2, 2, 4, 2, 2, 5, 5, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23] 100 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, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/619 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000566512750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566512750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000566512750 none CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 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, 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: [24, 24, 24, 24, 17, 3, 17, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 24, 24, 24, 24, 26, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 3, 3, 2, 2, 4, 2, 2, 3, 3, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24] 100 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, 59, 60, 61, 62]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000566512750 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 Building ZINC000566512750 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000566512750 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 618) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000566512750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566512750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000566512750 none CC1(C)CN(C(=O)C2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 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, 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: [23, 23, 23, 23, 15, 5, 15, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 23, 23, 23, 23, 26, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 5, 5, 2, 2, 4, 2, 2, 5, 5, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23] 100 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, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 619) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21) `ZINC000566512750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566512750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000566512750 none CC1(C)CN(C(=O)C2CN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)C2)c2ccc(N3CCOCC3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 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, 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: [24, 24, 24, 24, 17, 3, 17, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 24, 24, 24, 24, 26, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 3, 3, 2, 2, 4, 2, 2, 3, 3, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24] 100 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, 59, 60, 61, 62]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000566512750 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000566512750 Building ZINC000571820933 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571820933 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/620 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/620' -> `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)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1) `ZINC000571820933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571820933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000571820933 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 4, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 34, 34, 34, 34, 34, 23, 23, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 34, 34, 34, 34, 34, 23, 2, 2] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/621 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/621' -> `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)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1) `ZINC000571820933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571820933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000571820933 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 4, 4, 5, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 33, 33, 33, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 33, 33, 33, 17, 4, 4] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000571820933 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 Building ZINC000571820933 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000571820933 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 620) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1) `ZINC000571820933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000571820933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000571820933 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 4, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 34, 34, 34, 34, 34, 23, 23, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 34, 34, 34, 34, 34, 23, 2, 2] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 621) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1) `ZINC000571820933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000571820933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000571820933 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3ccc(c4cnn(C)c4)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 4, 4, 5, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 33, 33, 33, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 33, 33, 33, 33, 33, 17, 4, 4] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000571820933 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000571820933 Building ZINC000577964510 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577964510 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/622 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1) `ZINC000577964510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577964510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000577964510 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 9, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/623 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1) `ZINC000577964510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577964510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000577964510 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 10, 10, 10, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 10, 10, 4, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000577964510 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 Building ZINC000577964510 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577964510 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 622) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1) `ZINC000577964510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577964510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000577964510 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 9, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 623) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1) `ZINC000577964510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577964510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000577964510 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(c5cnn(C)c5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 10, 10, 10, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 10, 10, 4, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000577964510 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000577964510 Building ZINC000581895902 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000581895902 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/624 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1) `ZINC000581895902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000581895902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000581895902 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 12, 12, 12, 12, 12, 12, 12, 14, 35, 35, 35, 35, 35, 12, 12, 12, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 2, 2, 3] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68, 69, 70]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/625 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1) `ZINC000581895902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000581895902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000581895902 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 1, 1, 1, 2, 2, 3, 3, 5, 10, 10, 12, 12, 12, 12, 12, 12, 12, 14, 35, 35, 35, 35, 35, 12, 12, 12, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000581895902 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 Building ZINC000581895902 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000581895902 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 624) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1) `ZINC000581895902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000581895902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000581895902 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 12, 12, 12, 12, 12, 12, 12, 14, 35, 35, 35, 35, 35, 12, 12, 12, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 2, 2, 3] 50 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68, 69, 70]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 625) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1) `ZINC000581895902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000581895902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000581895902 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4cc(N5CCOCC5)ccc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 1, 1, 1, 2, 2, 3, 3, 5, 10, 10, 12, 12, 12, 12, 12, 12, 12, 14, 35, 35, 35, 35, 35, 12, 12, 12, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 3, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000581895902 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000581895902 Building ZINC000582014924 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000582014924 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/626 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/626' -> `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)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1) `ZINC000582014924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000582014924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000582014924 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 4, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 35, 35, 35, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 35, 35, 35, 17, 17, 2, 2] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/627 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/627' -> `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)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1) `ZINC000582014924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000582014924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000582014924 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 4, 4, 5, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 15, 15, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 15, 4, 4] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000582014924 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 Building ZINC000582014924 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000582014924 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 626) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1) `ZINC000582014924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000582014924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000582014924 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 4, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 35, 35, 35, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 35, 35, 35, 17, 17, 2, 2] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 627) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1) `ZINC000582014924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000582014924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000582014924 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(c4cnn(C)c4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 4, 4, 5, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 15, 15, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 15, 4, 4] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000582014924 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582014924 Building ZINC000582371819 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000582371819 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/628 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1) `ZINC000582371819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000582371819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000582371819 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 16, 16, 3, 4, 4, 7, 7, 7, 7, 7, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 16, 3, 3, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/629 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1) `ZINC000582371819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000582371819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000582371819 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 14, 14, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 14, 4, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000582371819 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 Building ZINC000582371819 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000582371819 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 628) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1) `ZINC000582371819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000582371819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000582371819 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 16, 16, 3, 4, 4, 7, 7, 7, 7, 7, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 16, 3, 3, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 629) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1) `ZINC000582371819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000582371819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000582371819 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C(=O)N3CC(C)(C)c4ccc(c5cnn(C)c5)cc43)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 5, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 14, 14, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 14, 4, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000582371819 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000582371819 Building ZINC000583576465 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000583576465 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/630 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1) `ZINC000583576465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000583576465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000583576465 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 18, 18, 18, 18, 18, 18, 18, 21, 50, 50, 50, 50, 50, 18, 18, 18, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 3, 3] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/631 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1) `ZINC000583576465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000583576465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000583576465 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 20, 20, 20, 20, 20, 20, 20, 23, 50, 50, 50, 50, 50, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 2, 2] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000583576465 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 Building ZINC000583576465 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000583576465 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 630) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1) `ZINC000583576465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000583576465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000583576465 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 5, 12, 12, 18, 18, 18, 18, 18, 18, 18, 21, 50, 50, 50, 50, 50, 18, 18, 18, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 3, 3] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 631) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1) `ZINC000583576465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000583576465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000583576465 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC(C(=O)N2CC(C)(C)c3cc(N4CCOCC4)ccc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 20, 20, 20, 20, 20, 20, 20, 23, 50, 50, 50, 50, 50, 20, 20, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 2, 2] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000583576465 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000583576465 Building ZINC000588047059 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588047059 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/632 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/632' -> `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)NCCNC(=O)c1cnccn1) `ZINC000588047059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588047059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000588047059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 9, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 9, 9, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/633 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/633' -> `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)NCCNC(=O)c1cnccn1) `ZINC000588047059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588047059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000588047059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 10, 10, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588047059 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 Building ZINC000588047059 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000588047059 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 632) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnccn1) `ZINC000588047059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588047059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000588047059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 9, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 9, 9, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 633) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnccn1) `ZINC000588047059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588047059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000588047059 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 10, 10, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588047059 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588047059 Building ZINC000588759581 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759581 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/634 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/635 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/636 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/636' -> `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)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/637 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/637' -> `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)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759581 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 Building ZINC000588759581 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759581 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 634) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 635) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 636) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 637) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759581 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 Building ZINC000588759581 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759581 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 634) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 635) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 636) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 637) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759581 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 Building ZINC000588759581 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759581 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 634) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 635) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 636) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 637) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1) `ZINC000588759581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759581 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 19, 19, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759581 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759581 Building ZINC000588759595 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759595 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/638 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/638' -> `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)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/639 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/639' -> `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)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/640 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/640' -> `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)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/641 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/641' -> `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)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759595 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 Building ZINC000588759595 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759595 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 638) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 639) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 640) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 641) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759595 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 Building ZINC000588759595 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759595 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 638) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 639) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 640) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 641) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759595 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 Building ZINC000588759595 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000588759595 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 638) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 639) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 640) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 641) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1) `ZINC000588759595.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000588759595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000588759595 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 6, 6, 3, 6, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8, 18, 18, 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, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000588759595 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000588759595 Building ZINC000589035849 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589035849 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/642 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589035849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589035849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589035849 none COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 5, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 26, 26, 13, 26, 26, 6, 6, 6, 6, 6, 16, 16, 16, 10, 10, 5, 5, 4, 4, 2, 2, 2, 2, 6, 6, 11, 11, 26, 26, 26, 26, 26, 18] 150 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]) total number of confs: 179 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/643 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589035849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589035849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589035849 none COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 25, 25, 15, 25, 25, 6, 6, 6, 6, 6, 14, 14, 14, 9, 9, 4, 4, 4, 4, 2, 2, 2, 2, 6, 6, 11, 11, 25, 25, 25, 25, 25, 18] 150 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]) total number of confs: 164 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589035849 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 Building ZINC000589035849 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589035849 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 642) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589035849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589035849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589035849 none COCCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 5, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 26, 26, 13, 26, 26, 6, 6, 6, 6, 6, 16, 16, 16, 10, 10, 5, 5, 4, 4, 2, 2, 2, 2, 6, 6, 11, 11, 26, 26, 26, 26, 26, 18] 150 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]) total number of confs: 179 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 643) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589035849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589035849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000589035849 none COCCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 25, 25, 15, 25, 25, 6, 6, 6, 6, 6, 14, 14, 14, 9, 9, 4, 4, 4, 4, 2, 2, 2, 2, 6, 6, 11, 11, 25, 25, 25, 25, 25, 18] 150 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]) total number of confs: 164 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589035849 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589035849 Building ZINC000589036095 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589036095 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/644 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O) `ZINC000589036095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589036095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589036095 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 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: [48, 39, 16, 8, 8, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 48, 48, 48, 39, 39, 16, 16, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 24] 150 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: 223 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/645 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O) `ZINC000589036095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589036095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589036095 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 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: [48, 39, 16, 8, 8, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 48, 48, 48, 39, 39, 16, 16, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 24] 150 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: 223 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589036095 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 Building ZINC000589036095 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589036095 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 644) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O) `ZINC000589036095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589036095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589036095 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 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: [48, 39, 16, 8, 8, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 48, 48, 48, 39, 39, 16, 16, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 24] 150 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: 223 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 645) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O) `ZINC000589036095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589036095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589036095 none COCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 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: [48, 39, 16, 8, 8, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 48, 48, 48, 39, 39, 16, 16, 8, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 24] 150 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: 223 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589036095 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036095 Building ZINC000589036170 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589036170 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/646 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589036170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589036170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589036170 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 4, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 9, 9, 9, 9, 17, 31, 31, 20, 31, 31, 9, 9, 9, 9, 9, 13, 13, 13, 8, 8, 4, 4, 2, 2, 2, 2, 9, 9, 17, 17, 31, 31, 31, 31, 31, 27] 150 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/647 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589036170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589036170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589036170 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [15, 10, 5, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 10, 10, 10, 10, 18, 32, 32, 21, 32, 32, 10, 10, 10, 10, 10, 15, 15, 15, 10, 10, 5, 5, 2, 2, 2, 2, 10, 10, 18, 18, 32, 32, 32, 32, 32, 30] 150 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589036170 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 Building ZINC000589036170 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589036170 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 646) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589036170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589036170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589036170 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 4, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 9, 9, 9, 9, 17, 31, 31, 20, 31, 31, 9, 9, 9, 9, 9, 13, 13, 13, 8, 8, 4, 4, 2, 2, 2, 2, 9, 9, 17, 17, 31, 31, 31, 31, 31, 27] 150 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 647) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000589036170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589036170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589036170 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 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: [15, 10, 5, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 10, 10, 10, 10, 18, 32, 32, 21, 32, 32, 10, 10, 10, 10, 10, 15, 15, 15, 10, 10, 5, 5, 2, 2, 2, 2, 10, 10, 18, 18, 32, 32, 32, 32, 32, 30] 150 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589036170 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036170 Building ZINC000589036450 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589036450 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/648 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589036450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589036450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000589036450 none O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 28, 28, 33, 40, 40, 40, 40, 34, 7, 8, 8, 12, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 8, 40, 40, 40, 40, 40, 40, 40, 40, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/649 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589036450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589036450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000589036450 none O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 29, 29, 34, 41, 41, 41, 41, 35, 7, 8, 8, 12, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 8, 41, 41, 41, 41, 41, 41, 41, 41, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589036450 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 Building ZINC000589036450 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589036450 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 648) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589036450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589036450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000589036450 none O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 28, 28, 33, 40, 40, 40, 40, 34, 7, 8, 8, 12, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 8, 40, 40, 40, 40, 40, 40, 40, 40, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 649) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589036450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589036450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC000589036450 none O=C(Nc1cc(S(=O)(=O)N2CCOCC2)ccc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 29, 29, 34, 41, 41, 41, 41, 35, 7, 8, 8, 12, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 8, 41, 41, 41, 41, 41, 41, 41, 41, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589036450 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589036450 Building ZINC000589037742 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589037742 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/650 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589037742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589037742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000589037742 none O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/651 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589037742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589037742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000589037742 none O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 15, 15, 15, 15, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589037742 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 Building ZINC000589037742 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589037742 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 650) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589037742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589037742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000589037742 none O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 651) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589037742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589037742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000589037742 none O=C(N1CCN(S(=O)(=O)c2cccc3nsnc32)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 15, 15, 15, 15, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589037742 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589037742 Building ZINC000589040408 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589040408 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/652 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589040408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589040408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589040408 none COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 28, 28, 34, 48, 48, 48, 48, 48, 39, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 4, 3, 3, 3, 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, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/653 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589040408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589040408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589040408 none COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 28, 28, 33, 48, 48, 48, 48, 48, 40, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 4, 3, 3, 3, 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, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589040408 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 Building ZINC000589040408 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589040408 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 652) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589040408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589040408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589040408 none COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 28, 28, 34, 48, 48, 48, 48, 48, 39, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 4, 3, 3, 3, 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, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 653) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589040408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589040408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000589040408 none COc1ccc(S(=O)(=O)N2CCN(C)CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 10, 10, 10, 10, 10, 28, 28, 33, 48, 48, 48, 48, 48, 40, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 4, 3, 3, 3, 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, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589040408 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589040408 Building ZINC000589041761 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589041761 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/654 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589041761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589041761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589041761 none O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 15, 15, 15, 15, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 45, 46, 47, 48, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/655 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589041761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589041761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589041761 none O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 22, 22, 22, 22, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1] 50 rigid atoms, others: [1, 45, 46, 47, 48, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589041761 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 Building ZINC000589041761 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589041761 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 654) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589041761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589041761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589041761 none O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 15, 15, 15, 15, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 45, 46, 47, 48, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 655) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589041761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589041761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000589041761 none O=C(N1CCN(S(=O)(=O)c2cc3c(cc2Cl)NC(=O)CO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 8, 22, 22, 22, 22, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1] 50 rigid atoms, others: [1, 45, 46, 47, 48, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/194367/xbs-8058088.45/working/building/ZINC000589041761 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589041761 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589041761 Building ZINC000589090463 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589090463 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/656 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1) `ZINC000589090463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589090463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589090463 none COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 46, 46, 46, 50, 23, 11, 23, 23, 11, 11, 11, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 46, 50, 50, 50, 46, 46, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 46] 50 rigid atoms, others: [42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/657 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1) `ZINC000589090463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589090463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589090463 none COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 27, 15, 27, 27, 15, 15, 15, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 49, 50, 50, 50, 49, 49, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15, 49] 50 rigid atoms, others: [42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589090463 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 Building ZINC000589090463 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589090463 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 656) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1) `ZINC000589090463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589090463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589090463 none COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 46, 46, 46, 50, 23, 11, 23, 23, 11, 11, 11, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 46, 50, 50, 50, 46, 46, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 46] 50 rigid atoms, others: [42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 657) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1) `ZINC000589090463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589090463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000589090463 none COc1ccc(OC)c(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 27, 15, 27, 27, 15, 15, 15, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 49, 50, 50, 50, 49, 49, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15, 49] 50 rigid atoms, others: [42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/194367/xbs-8058088.45/working/building/ZINC000589090463 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589090463 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589090463 Building ZINC000589117697 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589117697 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/658 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589117697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589117697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589117697 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 13, 13, 13, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/659 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589117697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589117697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589117697 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 15, 15, 15, 15, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589117697 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 Building ZINC000589117697 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000589117697 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 658) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589117697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000589117697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589117697 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 13, 13, 13, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 659) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000589117697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000589117697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000589117697 none O=C(N1CCCN(S(=O)(=O)c2ccc3c(c2)OCCO3)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 15, 15, 15, 15, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 49, 50, 51, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000589117697 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000589117697 Building ZINC000590281998 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590281998 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/660 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1) `ZINC000590281998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590281998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000590281998 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 30, 29, 9, 9, 15, 15, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 30, 30, 15, 15, 9, 9, 7, 7, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/661 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1) `ZINC000590281998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590281998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000590281998 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 31, 30, 16, 10, 16, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 31, 31, 16, 16, 10, 10, 8, 8, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000590281998 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 Building ZINC000590281998 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000590281998 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 660) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1) `ZINC000590281998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000590281998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000590281998 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 30, 29, 9, 9, 15, 15, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 30, 30, 15, 15, 9, 9, 7, 7, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 661) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1) `ZINC000590281998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000590281998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000590281998 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 31, 30, 16, 10, 16, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 31, 31, 16, 16, 10, 10, 8, 8, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000590281998 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000590281998 Building ZINC000591087763 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591087763 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/662 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/662' -> `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(CS(N)(=O)=O)CC1) `ZINC000591087763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591087763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000591087763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CS(N)(=O)=O)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 14, 8, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 5, 8, 8, 8, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4, 4, 5, 5, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/663 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/663' -> `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(CS(N)(=O)=O)CC1) `ZINC000591087763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591087763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000591087763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CS(N)(=O)=O)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 14, 8, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 6, 12, 12, 12, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591087763 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 Building ZINC000591087763 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000591087763 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 662) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CS(N)(=O)=O)CC1) `ZINC000591087763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591087763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000591087763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CS(N)(=O)=O)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 14, 8, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 5, 8, 8, 8, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4, 4, 5, 5, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 663) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CS(N)(=O)=O)CC1) `ZINC000591087763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591087763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000591087763 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CS(N)(=O)=O)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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 14, 8, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 6, 12, 12, 12, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591087763 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591087763 Building ZINC000591210557 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591210557 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/664 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/664' -> `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)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/665 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/665' -> `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)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 43, 43, 43, 43, 43, 44, 44, 43, 43, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 43, 43, 43, 43, 44, 44, 43, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/666 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/666' -> `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)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 25, 25, 25, 25, 25, 27, 44, 44, 44, 44, 44, 45, 45, 44, 44, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 3, 12, 12, 25, 25, 25, 44, 44, 44, 44, 45, 45, 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, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/667 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/667' -> `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)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 24, 24, 24, 24, 24, 25, 42, 42, 42, 42, 42, 43, 43, 42, 42, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 24, 24, 24, 42, 42, 42, 42, 43, 43, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591210557 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 Building ZINC000591210557 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591210557 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 664) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 665) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 43, 43, 43, 43, 43, 44, 44, 43, 43, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 43, 43, 43, 43, 44, 44, 43, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 666) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 25, 25, 25, 25, 25, 27, 44, 44, 44, 44, 44, 45, 45, 44, 44, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 3, 12, 12, 25, 25, 25, 44, 44, 44, 44, 45, 45, 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, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 667) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 24, 24, 24, 24, 24, 25, 42, 42, 42, 42, 42, 43, 43, 42, 42, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 24, 24, 24, 42, 42, 42, 42, 43, 43, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591210557 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 Building ZINC000591210557 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591210557 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 664) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 665) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 43, 43, 43, 43, 43, 44, 44, 43, 43, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 43, 43, 43, 43, 44, 44, 43, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 666) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 25, 25, 25, 25, 25, 27, 44, 44, 44, 44, 44, 45, 45, 44, 44, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 3, 12, 12, 25, 25, 25, 44, 44, 44, 44, 45, 45, 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, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 667) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 24, 24, 24, 24, 24, 25, 42, 42, 42, 42, 42, 43, 43, 42, 42, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 24, 24, 24, 42, 42, 42, 42, 43, 43, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591210557 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 Building ZINC000591210557 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591210557 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 664) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 665) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 25, 25, 25, 25, 25, 26, 43, 43, 43, 43, 43, 44, 44, 43, 43, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 25, 25, 25, 43, 43, 43, 43, 44, 44, 43, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 666) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 25, 25, 25, 25, 25, 27, 44, 44, 44, 44, 44, 45, 45, 44, 44, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 3, 12, 12, 25, 25, 25, 44, 44, 44, 44, 45, 45, 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, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 667) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)CC1) `ZINC000591210557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591210557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000591210557 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccnc1[N@]1CC[C@@H](C(N)=O)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 24, 24, 24, 24, 24, 25, 42, 42, 42, 42, 42, 43, 43, 42, 42, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 11, 11, 24, 24, 24, 42, 42, 42, 42, 43, 43, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591210557 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591210557 Building ZINC000591215915 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591215915 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/668 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/668' -> `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)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 21, 21, 21, 21, 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, 60, 61, 62, 63, 64]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/669 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/669' -> `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)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/670 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/670' -> `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)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 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, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/671 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/671' -> `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)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 14, 21, 26, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 14, 14, 26, 26, 26, 26, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591215915 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 Building ZINC000591215915 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591215915 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 668) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 21, 21, 21, 21, 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, 60, 61, 62, 63, 64]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 669) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 670) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 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, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 671) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 14, 21, 26, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 14, 14, 26, 26, 26, 26, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591215915 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 Building ZINC000591215915 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591215915 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 668) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 21, 21, 21, 21, 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, 60, 61, 62, 63, 64]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 669) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 670) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 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, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 671) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 14, 21, 26, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 14, 14, 26, 26, 26, 26, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591215915 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 Building ZINC000591215915 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000591215915 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 668) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 21, 21, 21, 21, 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, 60, 61, 62, 63, 64]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 669) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 670) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 20, 20, 20, 20, 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, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 671) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)CC1) `ZINC000591215915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000591215915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000591215915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2ncccn2)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', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] 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, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 14, 21, 26, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 14, 14, 26, 26, 26, 26, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000591215915 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000591215915 Building ZINC000594183056 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183056 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/672 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/672' -> `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)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/673 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/673' -> `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)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/674 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/674' -> `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)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/675 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/675' -> `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)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183056 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 Building ZINC000594183056 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183056 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 672) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 673) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 674) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 675) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183056 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 Building ZINC000594183056 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183056 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 672) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 673) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 674) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 675) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183056 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 Building ZINC000594183056 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183056 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 672) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 673) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 674) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 14, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 675) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O) `ZINC000594183056.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183056 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183056 Building ZINC000594183057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/676 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/676' -> `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)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/677 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/677' -> `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)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/678 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/678' -> `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)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/679 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/679' -> `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)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 Building ZINC000594183057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 676) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 677) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 678) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 679) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 Building ZINC000594183057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 676) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 677) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 678) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 679) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 Building ZINC000594183057 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000594183057 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 676) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 677) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 678) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 15, 15, 15, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 14, 14, 15, 15, 15, 15, 15, 15, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 679) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O) `ZINC000594183057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000594183057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594183057 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCN1CCC[C@@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 9, 9, 5, 9, 3, 3, 3, 2, 10, 10, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000594183057 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000594183057 Building ZINC000604190786 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604190786 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/680 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1) `ZINC000604190786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604190786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000604190786 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 4, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 16, 16, 31, 31, 27, 31, 31, 31, 9, 9, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 9, 9, 9, 9, 31, 31, 31, 31, 9, 9, 9, 9, 4] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/681 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1) `ZINC000604190786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604190786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000604190786 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 14, 14, 28, 28, 28, 28, 28, 28, 9, 9, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000604190786 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 Building ZINC000604190786 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000604190786 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 680) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1) `ZINC000604190786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000604190786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000604190786 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 4, 4, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 16, 16, 31, 31, 27, 31, 31, 31, 9, 9, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 9, 9, 9, 9, 31, 31, 31, 31, 9, 9, 9, 9, 4] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 681) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1) `ZINC000604190786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000604190786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000604190786 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)c3ccccc3I)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 2, 4, 6, 9, 9, 9, 9, 14, 14, 28, 28, 28, 28, 28, 28, 9, 9, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000604190786 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000604190786 Building ZINC000608895712 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608895712 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/682 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1) `ZINC000608895712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608895712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000608895712 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 29, 49, 29, 38, 38, 15, 9, 15, 15, 9, 9, 9, 3, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 38, 38, 50, 50, 50, 50, 50, 38, 38, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9, 9, 9, 38, 38] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/683 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1) `ZINC000608895712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608895712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000608895712 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 33, 49, 33, 46, 46, 18, 11, 18, 18, 11, 11, 11, 3, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 46, 46, 50, 50, 50, 50, 50, 46, 46, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 46, 46] 50 rigid atoms, others: [42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000608895712 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 Building ZINC000608895712 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000608895712 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 682) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1) `ZINC000608895712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000608895712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000608895712 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 29, 49, 29, 38, 38, 15, 9, 15, 15, 9, 9, 9, 3, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 38, 38, 50, 50, 50, 50, 50, 38, 38, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9, 9, 9, 38, 38] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 683) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1) `ZINC000608895712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000608895712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000608895712 none CCOC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 33, 49, 33, 46, 46, 18, 11, 18, 18, 11, 11, 11, 3, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 46, 46, 50, 50, 50, 50, 50, 46, 46, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 46, 46] 50 rigid atoms, others: [42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000608895712 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000608895712 Building ZINC000611924344 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611924344 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/684 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000611924344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611924344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000611924344 none COCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 6, 6, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 10, 10, 6, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 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, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/685 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000611924344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611924344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000611924344 none COCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 6, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 11, 11, 11, 11, 11, 6, 3, 3, 3, 3, 3, 2, 2, 2, 7, 7, 4, 7, 2, 2, 2, 3, 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, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000611924344 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 Building ZINC000611924344 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000611924344 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 684) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000611924344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000611924344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000611924344 none COCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 6, 6, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 10, 10, 6, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 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, 52, 53, 54, 55, 56, 57]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 685) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000611924344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000611924344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000611924344 none COCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 6, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 3, 3, 11, 11, 11, 11, 11, 6, 3, 3, 3, 3, 3, 2, 2, 2, 7, 7, 4, 7, 2, 2, 2, 3, 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, 52, 53, 54, 55, 56, 57]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000611924344 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000611924344 Building ZINC000613174683 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613174683 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/686 `/scratch/xiaobo/194367/xbs-8058088.45/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)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1) `ZINC000613174683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613174683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000613174683 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 16, 16, 16, 33, 33, 30, 33, 33, 33, 11, 11, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 11, 11, 33, 33, 31, 33, 11, 11, 11, 11, 2] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/687 `/scratch/xiaobo/194367/xbs-8058088.45/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)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1) `ZINC000613174683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613174683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000613174683 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 14, 14, 14, 34, 34, 27, 34, 34, 34, 7, 7, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 34, 34, 27, 34, 7, 7, 7, 7, 5] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613174683 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 Building ZINC000613174683 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613174683 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 686) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1) `ZINC000613174683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613174683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000613174683 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 16, 16, 16, 33, 33, 30, 33, 33, 33, 11, 11, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 11, 11, 33, 33, 31, 33, 11, 11, 11, 11, 2] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 687) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1) `ZINC000613174683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613174683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000613174683 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 14, 14, 14, 34, 34, 27, 34, 34, 34, 7, 7, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 7, 7, 7, 7, 34, 34, 27, 34, 7, 7, 7, 7, 5] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613174683 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613174683 Building ZINC000613624905 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613624905 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/688 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000613624905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613624905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000613624905 none Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 6, 14, 14, 6, 6, 6, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 6, 32] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/689 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000613624905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613624905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000613624905 none Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 11, 17, 17, 11, 11, 11, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 11, 35] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613624905 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 Building ZINC000613624905 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613624905 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 688) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000613624905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613624905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000613624905 none Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 6, 14, 14, 6, 6, 6, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 6, 32] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 689) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000613624905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613624905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000613624905 none Cc1cnc2c(cccc2S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 11, 17, 17, 11, 11, 11, 4, 1, 6, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 11, 35] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613624905 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613624905 Building ZINC000613675077 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613675077 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/690 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1) `ZINC000613675077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613675077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 8, 8, 8, 8, 8, 8, 12, 14, 14, 14, 8, 3, 3, 3, 20, 20, 5, 20, 3, 3, 3, 8, 8, 8, 8, 8, 8, 12, 14, 14, 14, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/691 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1) `ZINC000613675077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613675077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 7, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 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]) total number of confs: 78 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613675077 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 Building ZINC000613675077 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613675077 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 690) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1) `ZINC000613675077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613675077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 8, 8, 8, 8, 8, 8, 12, 14, 14, 14, 8, 3, 3, 3, 20, 20, 5, 20, 3, 3, 3, 8, 8, 8, 8, 8, 8, 12, 14, 14, 14, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 691) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1) `ZINC000613675077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613675077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675077 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 7, 3, 3, 3, 22, 22, 22, 22, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 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]) total number of confs: 78 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613675077 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675077 Building ZINC000613675093 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613675093 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/692 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1) `ZINC000613675093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613675093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675093 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 7, 3, 3, 3, 23, 23, 4, 23, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 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]) total number of confs: 107 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/693 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1) `ZINC000613675093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613675093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675093 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 5, 6, 6, 6, 6, 6, 6, 12, 14, 14, 14, 6, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 14, 14, 14, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613675093 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 Building ZINC000613675093 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000613675093 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 692) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1) `ZINC000613675093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000613675093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675093 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 6, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 7, 3, 3, 3, 23, 23, 4, 23, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 15, 15, 15, 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]) total number of confs: 107 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 693) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1) `ZINC000613675093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000613675093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000613675093 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 5, 6, 6, 6, 6, 6, 6, 12, 14, 14, 14, 6, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 6, 6, 6, 6, 6, 6, 12, 14, 14, 14, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 86 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000613675093 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000613675093 Building ZINC000614044816 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614044816 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/694 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/694' -> `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)N1CCN(CC(=O)N2CCc3ccccc32)CC1) `ZINC000614044816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614044816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614044816 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCc3ccccc32)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', 'N.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 6, 6, 6, 6, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/695 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/695' -> `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)N1CCN(CC(=O)N2CCc3ccccc32)CC1) `ZINC000614044816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614044816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614044816 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCc3ccccc32)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', 'N.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 2, 2, 1, 1, 1, 1, 2, 6, 8, 8, 8, 8, 18, 30, 30, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 8, 8, 8, 8, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614044816 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 Building ZINC000614044816 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614044816 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 694) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCc3ccccc32)CC1) `ZINC000614044816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614044816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614044816 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCc3ccccc32)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', 'N.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 6, 6, 6, 6, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 695) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCc3ccccc32)CC1) `ZINC000614044816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614044816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614044816 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCc3ccccc32)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', 'N.3', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 2, 2, 1, 1, 1, 1, 2, 6, 8, 8, 8, 8, 18, 30, 30, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 8, 8, 8, 8, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614044816 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614044816 Building ZINC000614120952 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614120952 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/696 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)cc1) `ZINC000614120952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614120952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120952 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 15, 15, 11, 15, 15, 15, 15, 23, 47, 47, 47, 47, 47, 47, 15, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 7, 7, 15, 15, 23, 46, 46, 47, 47, 47, 47, 47, 47, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/697 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)cc1) `ZINC000614120952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614120952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120952 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 15, 15, 8, 12, 15, 15, 15, 22, 47, 48, 48, 48, 48, 48, 15, 15, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 8, 8, 15, 15, 22, 46, 46, 48, 48, 48, 48, 48, 48, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614120952 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 Building ZINC000614120952 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614120952 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 696) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)cc1) `ZINC000614120952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614120952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120952 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 15, 15, 11, 15, 15, 15, 15, 23, 47, 47, 47, 47, 47, 47, 15, 15, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 7, 7, 15, 15, 23, 46, 46, 47, 47, 47, 47, 47, 47, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 697) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)cc1) `ZINC000614120952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614120952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120952 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 15, 15, 8, 12, 15, 15, 15, 22, 47, 48, 48, 48, 48, 48, 15, 15, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 8, 8, 15, 15, 22, 46, 46, 48, 48, 48, 48, 48, 48, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614120952 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120952 Building ZINC000614120953 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614120953 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/698 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)cc1) `ZINC000614120953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614120953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120953 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 13, 10, 13, 13, 13, 13, 22, 48, 49, 49, 49, 49, 49, 13, 13, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 7, 7, 13, 13, 22, 47, 47, 49, 49, 49, 49, 49, 49, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/699 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)cc1) `ZINC000614120953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614120953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120953 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 16, 16, 11, 11, 16, 16, 16, 23, 50, 50, 50, 50, 50, 50, 16, 16, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 16, 16, 23, 47, 47, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 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/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614120953 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 Building ZINC000614120953 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614120953 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 698) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)cc1) `ZINC000614120953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614120953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120953 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 13, 10, 13, 13, 13, 13, 22, 48, 49, 49, 49, 49, 49, 13, 13, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 7, 7, 13, 13, 22, 47, 47, 49, 49, 49, 49, 49, 49, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 699) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)cc1) `ZINC000614120953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614120953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000614120953 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(=O)(=O)NC[C@H]2CCCO2)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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 16, 16, 11, 11, 16, 16, 16, 23, 50, 50, 50, 50, 50, 50, 16, 16, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 16, 16, 23, 47, 47, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 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/194367/xbs-8058088.45/working/building/ZINC000614120953 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614120953 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614120953 Building ZINC000614709919 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000614709919 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/700 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 22, 31, 10, 22, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 22, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/701 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 23, 31, 10, 23, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 23, 23, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/702 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/702' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 19, 8, 19, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/703 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/703' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 21, 8, 21, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614709919 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 Building ZINC000614709919 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000614709919 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 700) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 22, 31, 10, 22, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 22, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 701) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 23, 31, 10, 23, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 23, 23, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 702) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 19, 8, 19, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 703) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 21, 8, 21, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614709919 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 Building ZINC000614709919 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000614709919 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 700) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 22, 31, 10, 22, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 22, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 701) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 23, 31, 10, 23, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 23, 23, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 702) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 19, 8, 19, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 703) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 21, 8, 21, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614709919 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 Building ZINC000614709919 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000614709919 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 700) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 22, 31, 10, 22, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 22, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 701) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)N(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 31, 39, 23, 31, 10, 23, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 23, 23, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 702) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 19, 8, 19, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 703) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000614709919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000614709919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000614709919 none Cc1nn(C)c(C)c1C(=O)C(=O)Nc1cccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens 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, 21, 8, 21, 8, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3] 50 rigid atoms, others: [46, 47, 48, 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, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000614709919 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000614709919 Building ZINC000615190576 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615190576 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/704 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/704' -> `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)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1) `ZINC000615190576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615190576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000615190576 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 5, 11, 11, 11, 11, 35, 35, 35, 35, 35, 44, 44, 42, 44, 44, 44, 35, 35, 35, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 35, 44, 44, 44, 44, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/705 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/705' -> `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)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1) `ZINC000615190576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615190576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000615190576 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 5, 10, 11, 11, 11, 36, 36, 36, 36, 36, 38, 38, 37, 38, 38, 38, 36, 36, 36, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 36, 38, 38, 38, 38, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000615190576 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 Building ZINC000615190576 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615190576 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 704) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1) `ZINC000615190576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615190576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000615190576 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 5, 11, 11, 11, 11, 35, 35, 35, 35, 35, 44, 44, 42, 44, 44, 44, 35, 35, 35, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 35, 44, 44, 44, 44, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 705) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1) `ZINC000615190576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615190576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000615190576 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2nn3cc(c4ccc(F)cc4)nc3s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 5, 10, 11, 11, 11, 36, 36, 36, 36, 36, 38, 38, 37, 38, 38, 38, 36, 36, 36, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 36, 38, 38, 38, 38, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000615190576 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615190576 Building ZINC000615761138 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615761138 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/706 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(F)(F)F) `ZINC000615761138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615761138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000615761138 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 6, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/707 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(F)(F)F) `ZINC000615761138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615761138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000615761138 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 4, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000615761138 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 Building ZINC000615761138 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615761138 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 706) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(F)(F)F) `ZINC000615761138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615761138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000615761138 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 6, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 707) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(F)(F)F) `ZINC000615761138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615761138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000615761138 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 4, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000615761138 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000615761138 Building ZINC000641988648 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641988648 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/708 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/708' -> `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)NCCC(=O)N1CCOCC1) `ZINC000641988648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641988648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641988648 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 12, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 9, 9, 9, 9, 9, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 2, 4, 4, 4, 4, 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: 61 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/709 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/709' -> `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)NCCC(=O)N1CCOCC1) `ZINC000641988648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641988648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641988648 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000641988648 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 Building ZINC000641988648 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641988648 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 708) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1) `ZINC000641988648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641988648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641988648 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 12, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 9, 9, 9, 9, 9, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 2, 4, 4, 4, 4, 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: 61 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 709) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1) `ZINC000641988648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641988648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641988648 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000641988648 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000641988648 Building ZINC000642555481 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642555481 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/710 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C) `ZINC000642555481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642555481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000642555481 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 14, 14, 14, 14, 41, 43, 48, 48, 48, 48, 23, 23, 23, 14, 4, 4, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 14, 14, 43, 43, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [5, 6, 7, 40, 9, 10, 11, 8] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/711 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C) `ZINC000642555481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642555481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000642555481 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 15, 15, 15, 15, 43, 45, 49, 49, 49, 49, 24, 24, 24, 15, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 15, 15, 45, 45, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [43, 5, 6, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 8, 50, 51, 22, 41, 23, 49, 42] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000642555481 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 Building ZINC000642555481 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642555481 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 710) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C) `ZINC000642555481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642555481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000642555481 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 14, 14, 14, 14, 41, 43, 48, 48, 48, 48, 23, 23, 23, 14, 4, 4, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 14, 14, 43, 43, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [5, 6, 7, 40, 9, 10, 11, 8] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 711) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C) `ZINC000642555481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642555481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC000642555481 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 15, 15, 15, 15, 43, 45, 49, 49, 49, 49, 24, 24, 24, 15, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 15, 15, 45, 45, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [43, 5, 6, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 8, 50, 51, 22, 41, 23, 49, 42] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000642555481 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000642555481 Building ZINC000645092549 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645092549 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/712 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000645092549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645092549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000645092549 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O 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', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 5, 7, 7, 7, 7, 7, 7, 5, 10, 10, 10, 10, 24, 37, 37, 33, 37, 37, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 10, 10, 24, 24, 37, 37, 37, 37, 37, 30] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 171 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/713 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000645092549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645092549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000645092549 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O 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', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 5, 7, 7, 7, 7, 7, 7, 5, 10, 10, 10, 10, 24, 37, 37, 32, 37, 37, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 10, 10, 24, 24, 37, 37, 37, 37, 37, 30] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 173 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645092549 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 Building ZINC000645092549 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645092549 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 712) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000645092549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645092549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000645092549 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O 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', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 5, 7, 7, 7, 7, 7, 7, 5, 10, 10, 10, 10, 24, 37, 37, 33, 37, 37, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 10, 10, 24, 24, 37, 37, 37, 37, 37, 30] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 171 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 713) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O) `ZINC000645092549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645092549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000645092549 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1c(N)n(Cc2ccccc2)c(=O)nc1O 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', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 5, 7, 7, 7, 7, 7, 7, 5, 10, 10, 10, 10, 24, 37, 37, 32, 37, 37, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 10, 10, 24, 24, 37, 37, 37, 37, 37, 30] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 173 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645092549 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645092549 Building ZINC000645144470 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645144470 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/714 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/714' -> `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)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1) `ZINC000645144470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645144470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000645144470 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 14, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 1, 7, 21, 29, 29, 29, 39, 39, 29, 29, 39, 39, 39, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 21, 21, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [17, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/715 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/715' -> `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)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1) `ZINC000645144470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645144470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000645144470 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 14, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 1, 7, 21, 30, 30, 30, 41, 41, 30, 30, 41, 41, 41, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 21, 21, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [17, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645144470 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 Building ZINC000645144470 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645144470 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 714) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1) `ZINC000645144470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645144470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000645144470 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 14, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 1, 7, 21, 29, 29, 29, 39, 39, 29, 29, 39, 39, 39, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 21, 21, 28, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [17, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 715) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1) `ZINC000645144470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645144470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000645144470 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(SCC(=O)Nc2ccc(C)cc2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 14, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 1, 7, 21, 30, 30, 30, 41, 41, 30, 30, 41, 41, 41, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 21, 21, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [17, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645144470 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645144470 Building ZINC000645433083 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645433083 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/716 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645433083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645433083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000645433083 none CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 21, 10, 5, 5, 5, 5, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 21, 21, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15] 150 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: 167 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/717 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645433083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645433083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000645433083 none CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 22, 10, 5, 5, 5, 5, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 22, 22, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15] 150 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: 173 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645433083 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 Building ZINC000645433083 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645433083 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 716) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645433083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645433083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000645433083 none CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 21, 10, 5, 5, 5, 5, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 21, 21, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15] 150 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: 167 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 717) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645433083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645433083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000645433083 none CCCCn1c(N)c(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', '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.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 22, 10, 5, 5, 5, 5, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 22, 22, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15] 150 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: 173 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645433083 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645433083 Building ZINC000645848787 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645848787 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/718 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645848787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645848787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000645848787 none CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 6, 6, 6, 6, 4, 2, 4, 11, 14, 14, 13, 14, 14, 14, 15, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 10, 10, 6, 6, 11, 11, 14, 14, 14, 14, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/719 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645848787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645848787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000645848787 none CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 12, 7, 7, 7, 7, 5, 2, 5, 11, 15, 15, 13, 15, 15, 15, 15, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 12, 12, 7, 7, 11, 11, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 121 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645848787 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 Building ZINC000645848787 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000645848787 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 718) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645848787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000645848787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000645848787 none CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 6, 6, 6, 6, 4, 2, 4, 11, 14, 14, 13, 14, 14, 14, 15, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 10, 10, 6, 6, 11, 11, 14, 14, 14, 14, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 719) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC000645848787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000645848787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000645848787 none CCCCn1c(N)c(N(Cc2ccccc2OC)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 12, 7, 7, 7, 7, 5, 2, 5, 11, 15, 15, 13, 15, 15, 15, 15, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 12, 12, 7, 7, 11, 11, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 121 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000645848787 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000645848787 Building ZINC000647741572 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647741572 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/720 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/720' -> `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)N1CCN(CC(=O)NC(C)C)CC1) `ZINC000647741572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647741572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000647741572 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 6, 8, 8, 8, 9, 9, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 3, 3, 3, 3, 6, 6, 8, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/721 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/721' -> `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)N1CCN(CC(=O)NC(C)C)CC1) `ZINC000647741572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647741572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000647741572 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 11, 11, 11, 13, 13, 4, 4, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 4, 4, 4, 4, 7, 7, 11, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000647741572 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 Building ZINC000647741572 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647741572 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 720) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1) `ZINC000647741572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647741572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000647741572 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 6, 8, 8, 8, 9, 9, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 3, 3, 3, 3, 6, 6, 8, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 721) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1) `ZINC000647741572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647741572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000647741572 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(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', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 11, 11, 11, 13, 13, 4, 4, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 4, 4, 4, 4, 7, 7, 11, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000647741572 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000647741572 Building ZINC000648428573 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648428573 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/722 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648428573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428573 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 11, 11, 4, 4, 1, 1, 1, 3, 7, 7, 8, 8, 8, 8, 33, 34, 42, 42, 42, 42, 42, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 4, 8, 8, 42, 42, 42, 42, 42, 42, 42, 42, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/723 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648428573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428573 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 13, 13, 15, 15, 15, 15, 31, 31, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 121 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000648428573 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 Building ZINC000648428573 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648428573 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 722) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648428573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428573 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 11, 11, 4, 4, 1, 1, 1, 3, 7, 7, 8, 8, 8, 8, 33, 34, 42, 42, 42, 42, 42, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 4, 8, 8, 42, 42, 42, 42, 42, 42, 42, 42, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 723) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648428573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428573 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 13, 13, 15, 15, 15, 15, 31, 31, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 121 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000648428573 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428573 Building ZINC000648428574 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648428574 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/724 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648428574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428574 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 8, 9, 10, 10, 10, 10, 28, 29, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 119 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/725 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648428574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428574 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 11, 11, 4, 4, 1, 1, 1, 3, 7, 7, 8, 8, 8, 8, 32, 32, 37, 37, 37, 37, 37, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 4, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 118 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000648428574 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 Building ZINC000648428574 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648428574 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 724) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648428574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428574 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 8, 9, 10, 10, 10, 10, 28, 29, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 119 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 725) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21) `ZINC000648428574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648428574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000648428574 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C(=O)N2CCOCC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 12, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 11, 11, 4, 4, 1, 1, 1, 3, 7, 7, 8, 8, 8, 8, 32, 32, 37, 37, 37, 37, 37, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 4, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 118 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000648428574 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000648428574 Building ZINC000673644022 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000673644022 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/726 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1) `ZINC000673644022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000673644022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000673644022 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 16, 16, 16, 16, 27, 27, 27, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/727 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1) `ZINC000673644022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000673644022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000673644022 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 8, 18, 18, 18, 18, 26, 26, 26, 50, 50, 49, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000673644022 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 Building ZINC000673644022 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000673644022 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 726) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1) `ZINC000673644022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000673644022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000673644022 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 16, 16, 16, 16, 27, 27, 27, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 727) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1) `ZINC000673644022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000673644022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000673644022 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 8, 18, 18, 18, 18, 26, 26, 26, 50, 50, 49, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000673644022 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000673644022 Building ZINC000680682222 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680682222 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/728 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000680682222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680682222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000680682222 none CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 26, 22, 26, 31, 4, 22, 22, 4, 3, 4, 4, 4, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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, 61, 62]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/729 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000680682222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680682222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000680682222 none CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 20, 23, 27, 4, 20, 20, 4, 4, 4, 4, 4, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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, 61, 62]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000680682222 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 Building ZINC000680682222 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680682222 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 728) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000680682222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680682222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000680682222 none CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 26, 22, 26, 31, 4, 22, 22, 4, 3, 4, 4, 4, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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, 61, 62]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 729) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC000680682222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680682222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC000680682222 none CCN(CC)S(=O)(=O)c1ccc(N2CCCC2)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 20, 23, 27, 4, 20, 20, 4, 4, 4, 4, 4, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 28, 28, 28, 28, 28, 27, 27, 27, 27, 27, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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, 61, 62]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000680682222 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000680682222 Building ZINC000726771451 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000726771451 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/730 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/731 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/732 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/732' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [34, 34, 34, 22, 11, 22, 11, 11, 5, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 34, 34, 34, 34, 34, 34, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 34] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/733 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/733' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [31, 31, 31, 21, 11, 21, 11, 11, 4, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 31, 31, 31, 31, 31, 31, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 31] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000726771451 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 Building ZINC000726771451 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000726771451 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 730) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 731) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 732) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [34, 34, 34, 22, 11, 22, 11, 11, 5, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 34, 34, 34, 34, 34, 34, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 34] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 733) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [31, 31, 31, 21, 11, 21, 11, 11, 4, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 31, 31, 31, 31, 31, 31, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 31] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000726771451 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 Building ZINC000726771451 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000726771451 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 730) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 731) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 732) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [34, 34, 34, 22, 11, 22, 11, 11, 5, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 34, 34, 34, 34, 34, 34, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 34] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 733) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [31, 31, 31, 21, 11, 21, 11, 11, 4, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 31, 31, 31, 31, 31, 31, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 31] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000726771451 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 Building ZINC000726771451 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000726771451 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 730) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 731) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1) `ZINC000726771451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)N2CCc3cc(Cc4ccc(NC(=O)[C@]([O-])([SiH3])c5cnn(C)c5)cc4)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 16, 33, 16, 16, 16, 16, 16, 16, 16, 8, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 16, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 8, 16, 16, 38] 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, 60]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 732) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [34, 34, 34, 22, 11, 22, 11, 11, 5, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 34, 34, 34, 34, 34, 34, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 34] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 733) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1) `ZINC000726771451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000726771451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000726771451 none Cn1cc(C(=O)C(=O)Nc2ccc(Cc3ccc4c(c3)CCN4C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'N.pl3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [31, 31, 31, 21, 11, 21, 11, 11, 4, 4, 7, 7, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 31, 31, 31, 31, 31, 31, 11, 7, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 31] 50 rigid atoms, others: [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, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC000726771451 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000726771451 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000726771451 Building ZINC000729281087 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000729281087 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/734 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/734' -> `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)NCCc1nnc(S)n1C) `ZINC000729281087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000729281087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000729281087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 6, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 11, 11, 11, 11, 11, 11, 3, 3, 3, 13, 13, 12, 13, 3, 3, 3, 2, 6, 6, 9, 9, 33, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/735 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/735' -> `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)NCCc1nnc(S)n1C) `ZINC000729281087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000729281087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000729281087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 6, 6, 9, 9, 36, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000729281087 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 Building ZINC000729281087 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000729281087 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 734) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(S)n1C) `ZINC000729281087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000729281087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000729281087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 6, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 11, 11, 11, 11, 11, 11, 3, 3, 3, 13, 13, 12, 13, 3, 3, 3, 2, 6, 6, 9, 9, 33, 11, 11, 11] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 124 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 735) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc(S)n1C) `ZINC000729281087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000729281087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000729281087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 6, 6, 9, 9, 36, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000729281087 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000729281087 Building ZINC000736944121 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000736944121 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/736 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC) `ZINC000736944121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000736944121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000736944121 none CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 1, 1, 12, 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, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 25, 25, 25, 38, 45, 45, 45, 45, 45, 25, 25, 13, 8, 8, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 38, 38, 38] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/737 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC) `ZINC000736944121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000736944121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000736944121 none CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 1, 1, 12, 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, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 24, 24, 24, 32, 43, 43, 43, 43, 43, 24, 24, 13, 9, 9, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000736944121 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 Building ZINC000736944121 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000736944121 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 736) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC) `ZINC000736944121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000736944121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000736944121 none CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 1, 1, 12, 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, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 25, 25, 25, 38, 45, 45, 45, 45, 45, 25, 25, 13, 8, 8, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 38, 38, 38] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 737) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC) `ZINC000736944121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000736944121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000736944121 none CCOc1ccc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2=O)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 1, 1, 12, 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, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 24, 24, 24, 32, 43, 43, 43, 43, 43, 24, 24, 13, 9, 9, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000736944121 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000736944121 Building ZINC000748523127 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748523127 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/738 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1) `ZINC000748523127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748523127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000748523127 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 20, 31, 31, 31, 31, 31, 31, 46, 46, 44, 46, 46, 46, 31, 31, 6, 6, 6, 6, 6, 6, 3, 15, 15, 20, 20, 31, 46, 46, 46, 46, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/739 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1) `ZINC000748523127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748523127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000748523127 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 20, 30, 30, 30, 30, 30, 30, 46, 46, 43, 46, 46, 46, 30, 30, 6, 6, 6, 6, 6, 6, 3, 15, 15, 20, 20, 30, 46, 46, 46, 46, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748523127 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 Building ZINC000748523127 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748523127 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 738) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1) `ZINC000748523127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748523127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000748523127 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 20, 31, 31, 31, 31, 31, 31, 46, 46, 44, 46, 46, 46, 31, 31, 6, 6, 6, 6, 6, 6, 3, 15, 15, 20, 20, 31, 46, 46, 46, 46, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 739) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1) `ZINC000748523127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748523127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000748523127 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3cccc(Br)c3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 20, 30, 30, 30, 30, 30, 30, 46, 46, 43, 46, 46, 46, 30, 30, 6, 6, 6, 6, 6, 6, 3, 15, 15, 20, 20, 30, 46, 46, 46, 46, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748523127 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748523127 Building ZINC000748557473 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748557473 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/740 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1) `ZINC000748557473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748557473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000748557473 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 19, 26, 26, 26, 26, 26, 26, 28, 28, 26, 26, 47, 49, 49, 28, 28, 26, 26, 5, 5, 5, 5, 5, 5, 2, 14, 14, 19, 19, 26, 28, 28, 47, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/741 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1) `ZINC000748557473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748557473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000748557473 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 17, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 42, 43, 43, 24, 24, 22, 22, 5, 5, 5, 5, 5, 5, 2, 13, 13, 17, 17, 22, 24, 24, 43, 24, 24, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748557473 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 Building ZINC000748557473 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748557473 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 740) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1) `ZINC000748557473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748557473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000748557473 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 19, 26, 26, 26, 26, 26, 26, 28, 28, 26, 26, 47, 49, 49, 28, 28, 26, 26, 5, 5, 5, 5, 5, 5, 2, 14, 14, 19, 19, 26, 28, 28, 47, 28, 28, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 741) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1) `ZINC000748557473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748557473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000748557473 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc(OC(F)F)cc3)C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 17, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 42, 43, 43, 24, 24, 22, 22, 5, 5, 5, 5, 5, 5, 2, 13, 13, 17, 17, 22, 24, 24, 43, 24, 24, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748557473 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748557473 Building ZINC000748558302 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748558302 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/742 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F) `ZINC000748558302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748558302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000748558302 none COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 21, 21, 21, 21, 45, 50, 50, 39, 39, 39, 21, 12, 12, 12, 8, 8, 3, 3, 3, 3, 3, 3, 21, 21, 50] 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/743 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F) `ZINC000748558302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748558302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000748558302 none COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 10, 10, 10, 10, 10, 10, 10, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 20, 45, 50, 50, 37, 37, 37, 20, 10, 10, 10, 6, 6, 2, 3, 3, 3, 3, 3, 20, 20, 50] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748558302 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 Building ZINC000748558302 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748558302 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 742) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F) `ZINC000748558302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748558302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000748558302 none COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 21, 21, 21, 21, 45, 50, 50, 39, 39, 39, 21, 12, 12, 12, 8, 8, 3, 3, 3, 3, 3, 3, 21, 21, 50] 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 743) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F) `ZINC000748558302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748558302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000748558302 none COc1cc(/C=C2/SC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)C2=O)ccc1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.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.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 10, 10, 10, 10, 10, 10, 10, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 20, 20, 20, 20, 45, 50, 50, 37, 37, 37, 20, 10, 10, 10, 6, 6, 2, 3, 3, 3, 3, 3, 20, 20, 50] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748558302 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748558302 Building ZINC000748637182 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748637182 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/744 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)c2)cc1) `ZINC000748637182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748637182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748637182 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)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', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.o2', 'C.3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 5, 11, 11, 14, 5, 11, 11, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 6, 6, 6, 19, 19, 15, 19, 19, 38, 38, 38, 19, 39, 39, 39, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 6, 19, 19, 38, 38, 38, 39, 39, 39, 19, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/745 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)c2)cc1) `ZINC000748637182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748637182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748637182 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)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', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.o2', 'C.3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 5, 11, 11, 14, 5, 11, 11, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 6, 6, 6, 20, 20, 15, 17, 20, 39, 39, 39, 20, 39, 39, 39, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 39, 39, 39, 39, 39, 39, 20, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748637182 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 Building ZINC000748637182 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748637182 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 744) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)c2)cc1) `ZINC000748637182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748637182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748637182 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)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', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.o2', 'C.3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 5, 11, 11, 14, 5, 11, 11, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 6, 6, 6, 19, 19, 15, 19, 19, 38, 38, 38, 19, 39, 39, 39, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 6, 19, 19, 38, 38, 38, 39, 39, 39, 19, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 745) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)c2)cc1) `ZINC000748637182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748637182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000748637182 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N(S(C)(=O)=O)S(C)(=O)=O)c(Br)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', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.o2', 'C.3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 5, 11, 11, 14, 5, 11, 11, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 6, 6, 6, 20, 20, 15, 17, 20, 39, 39, 39, 20, 39, 39, 39, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 39, 39, 39, 39, 39, 39, 20, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000748637182 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000748637182 Building ZINC000751088203 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751088203 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/746 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c2n(c(c3cccc(NC(=O)[C@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2) `ZINC000751088203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751088203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000751088203 none COC(=O)c1c2n(c(c3cccc(NC(=O)[C@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 18, 44, 18, 18, 18, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 41, 41, 41, 18, 18, 18, 44, 44, 44, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 41, 41, 41, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/747 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c2n(c(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2) `ZINC000751088203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751088203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000751088203 none COC(=O)c1c2n(c(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 17, 41, 17, 17, 17, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 17, 17, 40, 40, 40, 17, 17, 17, 41, 41, 41, 4, 4, 4, 2, 5, 5, 5, 5, 5, 4, 40, 40, 40, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000751088203 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 Building ZINC000751088203 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751088203 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 746) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)c1c2n(c(c3cccc(NC(=O)[C@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2) `ZINC000751088203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751088203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000751088203 none COC(=O)c1c2n(c(c3cccc(NC(=O)[C@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 18, 44, 18, 18, 18, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 41, 41, 41, 18, 18, 18, 44, 44, 44, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 41, 41, 41, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 747) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)c1c2n(c(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2) `ZINC000751088203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751088203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000751088203 none COC(=O)c1c2n(c(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)c3)c1C(=O)OC)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 17, 41, 17, 17, 17, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 4, 17, 17, 40, 40, 40, 17, 17, 17, 41, 41, 41, 4, 4, 4, 2, 5, 5, 5, 5, 5, 4, 40, 40, 40, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000751088203 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751088203 Building ZINC000751384971 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751384971 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/748 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000751384971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751384971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000751384971 none CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 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.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 35, 31, 31, 18, 13, 9, 13, 13, 9, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 33, 31, 31, 31, 31, 18, 3, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/749 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000751384971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751384971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000751384971 none CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 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.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 35, 32, 32, 19, 14, 10, 14, 14, 10, 4, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 32, 32, 32, 32, 19, 4, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000751384971 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 Building ZINC000751384971 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751384971 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 748) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000751384971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751384971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000751384971 none CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 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.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 35, 31, 31, 18, 13, 9, 13, 13, 9, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 33, 31, 31, 31, 31, 18, 3, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 749) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000751384971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751384971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000751384971 none CC(C)(C)OC(=O)NCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 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.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 35, 32, 32, 19, 14, 10, 14, 14, 10, 4, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 32, 32, 32, 32, 19, 4, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000751384971 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000751384971 Building ZINC000916726920 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916726920 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/750 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)cn1) `ZINC000916726920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916726920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916726920 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 18, 33, 33, 33, 33, 33, 33, 39, 39, 39, 39, 39, 39, 39, 39, 33, 33, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 13, 13, 18, 18, 33, 39, 39, 39, 39, 39, 5] 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/751 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)cn1) `ZINC000916726920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916726920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916726920 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 17, 34, 34, 34, 34, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 13, 13, 17, 17, 34, 44, 44, 44, 44, 44, 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000916726920 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 Building ZINC000916726920 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916726920 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 750) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)cn1) `ZINC000916726920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916726920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916726920 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 18, 33, 33, 33, 33, 33, 33, 39, 39, 39, 39, 39, 39, 39, 39, 33, 33, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 13, 13, 18, 18, 33, 39, 39, 39, 39, 39, 5] 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 751) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)cn1) `ZINC000916726920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916726920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916726920 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCN2C(=O)S/C(=C/c3ccc4c(c3)OCO4)C2=O)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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 17, 34, 34, 34, 34, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 13, 13, 17, 17, 34, 44, 44, 44, 44, 44, 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000916726920 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916726920 Building ZINC000916728677 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916728677 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/752 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1) `ZINC000916728677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916728677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916728677 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 4, 4, 1, 1, 1, 1, 6, 10, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 24, 24, 24, 24, 25, 25, 25, 25, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/753 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1) `ZINC000916728677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916728677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916728677 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 5, 5, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000916728677 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 Building ZINC000916728677 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916728677 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 752) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1) `ZINC000916728677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916728677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916728677 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 4, 4, 1, 1, 1, 1, 6, 10, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 24, 24, 24, 24, 25, 25, 25, 25, 24, 24, 24, 24, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 753) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1) `ZINC000916728677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916728677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000916728677 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccccc3C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 5, 5, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000916728677 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000916728677 Building ZINC000917041375 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917041375 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/754 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000917041375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917041375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000917041375 none COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 14, 11, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 9, 9, 9, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 9, 9, 20, 18, 18, 18, 9, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 9, 20, 20, 20] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/755 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000917041375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917041375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000917041375 none COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 14, 11, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 9, 9, 21, 17, 17, 17, 9, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 9, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000917041375 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 Building ZINC000917041375 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917041375 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 754) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000917041375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917041375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000917041375 none COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 14, 11, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 9, 9, 9, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 9, 9, 20, 18, 18, 18, 9, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 9, 20, 20, 20] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 755) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC) `ZINC000917041375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917041375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000917041375 none COc1cc(Br)c(S(=O)(=O)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 14, 11, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 9, 9, 9, 9, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 9, 9, 9, 21, 17, 17, 17, 9, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 9, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000917041375 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000917041375 Building ZINC000918128492 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918128492 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/756 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/756' -> `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)NCCN1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000918128492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918128492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000918128492 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 5, 7, 7, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 18, 24, 24, 24, 24, 34, 34, 35, 35, 35, 35, 24, 24, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 2, 10, 10, 15, 15, 24, 24, 24, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/757 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/757' -> `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)NCCN1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000918128492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918128492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000918128492 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 18, 25, 25, 25, 25, 33, 33, 33, 33, 33, 33, 25, 25, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 11, 11, 14, 14, 25, 25, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000918128492 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 Building ZINC000918128492 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918128492 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 756) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000918128492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918128492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000918128492 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 5, 7, 7, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 18, 24, 24, 24, 24, 34, 34, 35, 35, 35, 35, 24, 24, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 4, 2, 10, 10, 15, 15, 24, 24, 24, 24, 35, 35, 35, 35, 35, 35, 35, 35, 35, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 757) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)OC(C)(C)C)CC1) `ZINC000918128492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918128492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC000918128492 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 18, 25, 25, 25, 25, 33, 33, 33, 33, 33, 33, 25, 25, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 11, 11, 14, 14, 25, 25, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000918128492 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918128492 Building ZINC000918384321 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918384321 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/758 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918384321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384321 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 26, 35, 26, 26, 26, 24, 4, 17, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 4, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 106 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/759 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918384321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384321 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 29, 21, 29, 21, 21, 21, 18, 3, 9, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 3, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 101 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000918384321 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 Building ZINC000918384321 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918384321 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 758) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918384321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384321 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 26, 35, 26, 26, 26, 24, 4, 17, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 2, 4, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 106 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 759) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918384321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384321 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 29, 21, 29, 21, 21, 21, 18, 3, 9, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 3, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 101 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000918384321 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384321 Building ZINC000918384322 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918384322 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/760 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918384322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384322 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 20, 27, 20, 20, 20, 18, 2, 9, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 2, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 2, 20, 20, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 94 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/761 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918384322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384322 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 41, 31, 41, 31, 31, 31, 24, 5, 16, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 5, 31, 31, 42, 42, 42, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 31, 31, 31, 31] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 117 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000918384322 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 Building ZINC000918384322 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918384322 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 760) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918384322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384322 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 20, 27, 20, 20, 20, 18, 2, 9, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 2, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 2, 20, 20, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 94 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 761) grep: /scratch/xiaobo/194367/xbs-8058088.45/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)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)CC1) `ZINC000918384322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918384322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 74 natoms 73 natoms 72 natoms 71 names: ZINC000918384322 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 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, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 41, 31, 41, 31, 31, 31, 24, 5, 16, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 5, 31, 31, 42, 42, 42, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 31, 31, 31, 31] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 117 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC000918384322 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC000918384322 Building ZINC001142279305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/762 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142279305 none O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 21, 21, 21, 21, 19, 21, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 5, 36, 36, 36, 8, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/763 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142279305 none O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 22, 22, 22, 22, 20, 22, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 5, 36, 36, 36, 8, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142279305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 Building ZINC001142279305 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279305 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 762) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142279305 none O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 21, 21, 21, 21, 19, 21, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 5, 36, 36, 36, 8, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 763) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142279305 none O=C(Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 22, 22, 22, 22, 20, 22, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 5, 36, 36, 36, 8, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142279305 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142279305 Building ZINC001142284153 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284153 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/764 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c2cc1C3) `ZINC001142284153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142284153 none CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c2cc1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 12, 5, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 31, 41, 41, 41, 41, 41, 93, 31, 31, 31, 31, 31, 31, 7, 10, 10, 10, 31, 31, 31] 150 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/765 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c2cc1C3) `ZINC001142284153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142284153 none CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c2cc1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 12, 5, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 31, 41, 41, 41, 41, 41, 93, 31, 31, 31, 31, 31, 31, 7, 10, 10, 10, 31, 31, 31] 150 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142284153 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 Building ZINC001142284153 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284153 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 764) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c2cc1C3) `ZINC001142284153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142284153 none CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@@]([O-])([SiH3])c4ccco4)c2cc1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 12, 5, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 31, 41, 41, 41, 41, 41, 93, 31, 31, 31, 31, 31, 31, 7, 10, 10, 10, 31, 31, 31] 150 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 765) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c2cc1C3) `ZINC001142284153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142284153 none CC[C@@]1(O)C(=O)OCc2c(=O)n3c(cc21)-c1nc2cccc(NC(=O)[C@]([O-])([SiH3])c4ccco4)c2cc1C3 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 12, 5, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 31, 41, 41, 41, 41, 41, 93, 31, 31, 31, 31, 31, 31, 7, 10, 10, 10, 31, 31, 31] 150 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142284153 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142284153 Building ZINC001142286822 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286822 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/766 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/767 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/768 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/768' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/769 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/769' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286822 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 Building ZINC001142286822 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286822 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 766) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 767) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 768) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 769) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286822 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 Building ZINC001142286822 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286822 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 766) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 767) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 768) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 769) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286822 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 Building ZINC001142286822 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286822 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 766) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 767) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 13, 13, 13, 13, 13, 13, 7, 10, 10, 10, 13, 23, 23, 23] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 768) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 769) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286822.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286822 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 12, 22, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 12, 12, 12, 12, 12, 12, 6, 10, 10, 10, 12, 22, 22, 22] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286822 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286822 Building ZINC001142286823 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286823 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/770 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/771 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/772 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/772' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/773 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/773' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286823 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 Building ZINC001142286823 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286823 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 770) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 771) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 772) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 773) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286823 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 Building ZINC001142286823 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286823 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 770) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 771) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 772) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 773) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286823 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 Building ZINC001142286823 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142286823 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 770) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 771) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 21, 11, 21, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 21, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 11, 27, 27, 27] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 772) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 773) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC) `ZINC001142286823.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142286823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001142286823 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 13, 23, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 23, 13, 13, 13, 13, 13, 13, 7, 9, 9, 9, 13, 28, 28, 28] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142286823 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142286823 Building ZINC001142287709 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287709 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/774 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN) `ZINC001142287709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142287709 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 5, 11, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 8, 8, 8, 23, 23, 26, 13, 13, 13, 8, 7, 7, 7, 8, 8, 8, 13, 13, 13, 13, 13, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/775 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN) `ZINC001142287709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142287709 none COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 5, 11, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 8, 8, 8, 24, 24, 26, 14, 14, 14, 8, 7, 7, 7, 8, 8, 8, 13, 13, 13, 13, 13, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142287709 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 Building ZINC001142287709 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287709 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 774) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN) `ZINC001142287709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142287709 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 5, 11, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 8, 8, 8, 23, 23, 26, 13, 13, 13, 8, 7, 7, 7, 8, 8, 8, 13, 13, 13, 13, 13, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 775) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN) `ZINC001142287709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142287709 none COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccco2)S(C)(=O)=O)c(Oc2ccccc2)cc1C(=O)CN NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 14, 5, 11, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 8, 8, 8, 24, 24, 26, 14, 14, 14, 8, 7, 7, 7, 8, 8, 8, 13, 13, 13, 13, 13, 8, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142287709 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142287709 Building ZINC001142290970 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290970 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/776 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1) `ZINC001142290970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001142290970 none CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', '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, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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] 0 hydrogens 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, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 8, 8, 8, 8, 20, 35, 35, 20, 35, 35, 17, 17, 17, 17, 17, 17, 17, 13, 13, 4, 9, 9, 9, 20, 20, 35, 35, 20, 35, 35, 17] 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/777 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1) `ZINC001142290970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001142290970 none CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', '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, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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] 0 hydrogens 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, 16, 17, 17, 16, 16, 16, 16, 11, 7, 3, 7, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 20, 27, 27, 20, 27, 27, 16, 17, 17, 17, 16, 16, 16, 11, 11, 3, 8, 8, 8, 20, 20, 27, 27, 20, 27, 27, 16] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142290970 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 Building ZINC001142290970 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290970 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 776) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1) `ZINC001142290970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001142290970 none CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', '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, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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] 0 hydrogens 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, 13, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 8, 8, 8, 8, 20, 35, 35, 20, 35, 35, 17, 17, 17, 17, 17, 17, 17, 13, 13, 4, 9, 9, 9, 20, 20, 35, 35, 20, 35, 35, 17] 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]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 777) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1) `ZINC001142290970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001142290970 none CS(=O)(=O)c1cccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccco2)C(=O)OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', '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, 14, 11, 11, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 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] 0 hydrogens 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, 16, 17, 17, 16, 16, 16, 16, 11, 7, 3, 7, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 7, 7, 7, 7, 20, 27, 27, 20, 27, 27, 16, 17, 17, 17, 16, 16, 16, 11, 11, 3, 8, 8, 8, 20, 20, 27, 27, 20, 27, 27, 16] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142290970 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290970 Building ZINC001142290996 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290996 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/778 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O) `ZINC001142290996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001142290996 none CCC(CC)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 4, 8, 10, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 16, 24, 24, 26, 26, 26, 26, 8, 8, 8, 8, 16, 16, 16, 8, 8, 8, 10, 10, 10, 10, 10, 8, 10, 10, 10, 10, 10, 2, 6, 6, 6, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 16, 16, 16, 24] 150 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 191 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/779 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O) `ZINC001142290996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001142290996 none CCC(CC)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 4, 9, 10, 3, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 7, 9, 9, 9, 9, 14, 22, 22, 24, 24, 24, 24, 9, 9, 9, 9, 17, 17, 17, 9, 9, 9, 10, 10, 10, 10, 10, 9, 10, 10, 10, 10, 10, 3, 5, 5, 5, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 17, 17, 17, 27] 150 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142290996 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 Building ZINC001142290996 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290996 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 778) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC(CC)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O) `ZINC001142290996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001142290996 none CCC(CC)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 4, 8, 10, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 16, 24, 24, 26, 26, 26, 26, 8, 8, 8, 8, 16, 16, 16, 8, 8, 8, 10, 10, 10, 10, 10, 8, 10, 10, 10, 10, 10, 2, 6, 6, 6, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 16, 16, 16, 24] 150 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 191 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 779) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC(CC)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O) `ZINC001142290996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001142290996 none CCC(CC)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@H]1[C@H](NC(=O)OC(C)(C)C)C[C@H](C(=O)OC)[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 4, 9, 10, 3, 4, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 7, 9, 9, 9, 9, 14, 22, 22, 24, 24, 24, 24, 9, 9, 9, 9, 17, 17, 17, 9, 9, 9, 10, 10, 10, 10, 10, 9, 10, 10, 10, 10, 10, 3, 5, 5, 5, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 17, 17, 17, 27] 150 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142290996 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142290996 Building ZINC001142688405 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688405 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/780 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001142688405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142688405 none Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 6, 6, 23, 23, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 23, 23, 23, 45, 45, 45, 23, 23, 37, 37, 37, 23, 40, 40, 23, 23, 23, 23, 6, 4, 4, 1, 4, 4, 23, 45, 37, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/781 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001142688405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142688405 none Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 6, 6, 22, 22, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 22, 22, 22, 46, 46, 46, 39, 39, 46, 46, 46, 39, 39, 39, 39, 39, 22, 22, 6, 4, 4, 1, 4, 4, 22, 46, 46, 39] 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]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142688405 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 Building ZINC001142688405 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688405 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 780) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001142688405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142688405 none Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 6, 6, 23, 23, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 23, 23, 23, 45, 45, 45, 23, 23, 37, 37, 37, 23, 40, 40, 23, 23, 23, 23, 6, 4, 4, 1, 4, 4, 23, 45, 37, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 781) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001142688405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142688405 none Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 6, 6, 22, 22, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 22, 22, 22, 46, 46, 46, 39, 39, 46, 46, 46, 39, 39, 39, 39, 39, 22, 22, 6, 4, 4, 1, 4, 4, 22, 46, 46, 39] 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]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142688405 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142688405 Building ZINC001142694479 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142694479 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/782 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142694479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142694479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142694479 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 22, 13, 21, 21, 31, 43, 43, 43, 43, 43, 43, 43, 43, 43, 13, 8, 13, 3, 8, 8, 18, 18, 18, 18, 18, 18, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 22, 22, 31, 31, 43, 43, 43, 43, 43, 13, 18, 18, 18, 18, 18, 18, 18, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 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: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/783 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142694479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142694479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142694479 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 9, 17, 17, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 6, 9, 3, 6, 6, 13, 13, 13, 13, 13, 13, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 18, 18, 27, 27, 40, 40, 40, 40, 40, 9, 13, 13, 13, 13, 13, 13, 13, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 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: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142694479 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 Building ZINC001142694479 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142694479 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 782) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142694479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142694479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142694479 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 22, 13, 21, 21, 31, 43, 43, 43, 43, 43, 43, 43, 43, 43, 13, 8, 13, 3, 8, 8, 18, 18, 18, 18, 18, 18, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 22, 22, 31, 31, 43, 43, 43, 43, 43, 13, 18, 18, 18, 18, 18, 18, 18, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 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: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 783) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142694479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142694479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001142694479 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'C.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 9, 17, 17, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 6, 9, 3, 6, 6, 13, 13, 13, 13, 13, 13, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 18, 18, 27, 27, 40, 40, 40, 40, 40, 9, 13, 13, 13, 13, 13, 13, 13, 3, 2, 2, 1, 2, 2] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 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: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142694479 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694479 Building ZINC001142694547 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142694547 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/784 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001142694547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142694547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142694547 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', '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, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 14, 14, 22, 27, 28, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 27, 27, 28, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/785 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001142694547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142694547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142694547 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', '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, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 10, 17, 17, 25, 28, 28, 32, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 17, 17, 17, 17, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 3, 5, 6, 7, 8, 9, 42, 11, 12, 13, 14, 15, 43, 44, 46, 47, 10] set([0, 1, 2, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142694547 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 Building ZINC001142694547 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142694547 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 784) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001142694547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142694547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142694547 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', '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, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 14, 14, 22, 27, 28, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 27, 27, 28, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 785) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001142694547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142694547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001142694547 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', '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, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 10, 17, 17, 25, 28, 28, 32, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 17, 17, 17, 17, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 3, 5, 6, 7, 8, 9, 42, 11, 12, 13, 14, 15, 43, 44, 46, 47, 10] set([0, 1, 2, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142694547 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142694547 Building ZINC001142702701 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702701 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/786 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(COCCN)N(C(=O)[C@@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001142702701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142702701 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 5, 12, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 1, 5, 1, 1, 1, 3, 9, 23, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 3, 3, 23, 23, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 6, 6, 6, 2, 2, 1, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 4, 8, 9, 10, 11, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/787 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(COCCN)N(C(=O)[C@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001142702701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142702701 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 5, 12, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 8, 26, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 15, 15, 15, 15, 15, 3, 3, 26, 26, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 6, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 4, 8, 9, 10, 11, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 204 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142702701 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 Building ZINC001142702701 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702701 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 786) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C(COCCN)N(C(=O)[C@@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001142702701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142702701 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 5, 12, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 5, 1, 5, 1, 1, 1, 3, 9, 23, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 3, 3, 23, 23, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 6, 6, 6, 2, 2, 1, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 4, 8, 9, 10, 11, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 787) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C(COCCN)N(C(=O)[C@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001142702701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142702701 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@](C)([O-])[SiH3])C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 5, 12, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 8, 26, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 15, 15, 15, 15, 15, 3, 3, 26, 26, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 6, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 4, 8, 9, 10, 11, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 204 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142702701 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702701 Building ZINC001142702870 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702870 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/788 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12) `ZINC001142702870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142702870 none C[C@@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 15, 21, 29, 29, 29, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 1, 1, 1, 3, 15, 15, 21, 21, 29, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/789 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12) `ZINC001142702870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142702870 none C[C@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 17, 24, 32, 32, 32, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 1, 1, 1, 3, 17, 17, 24, 24, 32, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142702870 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 Building ZINC001142702870 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702870 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 788) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12) `ZINC001142702870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142702870 none C[C@@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 15, 21, 29, 29, 29, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 1, 1, 1, 3, 15, 15, 21, 21, 29, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 789) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12) `ZINC001142702870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142702870 none C[C@]([O-])([SiH3])C(=O)NCCc1cn(S(=O)(=O)c2c(Cl)nc3sccn32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.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, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 17, 24, 32, 32, 32, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 1, 1, 1, 3, 17, 17, 24, 24, 32, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142702870 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702870 Building ZINC001142702963 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702963 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/790 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CCCN(C(=N)N)C(=O)[C@@](C)([O-])[SiH3])C(=O)SCc1ccccc1) `ZINC001142702963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 4 19 3 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142702963 none CC(C)(C)OC(=O)N[C@@H](CCCN(C(=N)N)C(=O)[C@@](C)([O-])[SiH3])C(=O)SCc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 8, 8, 1, 11, 5, 5, 12, 1, 11, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 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, 4, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 22, 19, 5, 19, 5, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 19, 27, 27, 45, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 5, 5, 5, 5, 4, 4, 4, 4, 4, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [51, 17, 19, 20, 21, 52, 53] 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, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 169 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/791 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CCCN(C(=N)N)C(=O)[C@](C)([O-])[SiH3])C(=O)SCc1ccccc1) `ZINC001142702963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: ZINC001142702963 failed due to unspecified stereochemistry with strict stereo enabled warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 Conformer generation produced nothing Skipping ZINC001142702963 1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 `1' -> `1.failed' Finished preparing ZINC001142702963 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Found failed protomers Marking ZINC001142702963 as failed mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/failed' `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963' -> `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963' Building ZINC001142702963 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702963 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 790) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CCCN(C(=N)N)C(=O)[C@@](C)([O-])[SiH3])C(=O)SCc1ccccc1) `ZINC001142702963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 4 19 3 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001142702963 none CC(C)(C)OC(=O)N[C@@H](CCCN(C(=N)N)C(=O)[C@@](C)([O-])[SiH3])C(=O)SCc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 8, 8, 1, 11, 5, 5, 12, 1, 11, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 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, 4, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 22, 19, 5, 19, 5, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 19, 27, 27, 45, 49, 49, 49, 49, 49, 49, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 5, 5, 5, 5, 4, 4, 4, 4, 4, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [51, 17, 19, 20, 21, 52, 53] 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, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 169 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 791) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CCCN(C(=N)N)C(=O)[C@](C)([O-])[SiH3])C(=O)SCc1ccccc1) `ZINC001142702963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: ZINC001142702963 failed due to unspecified stereochemistry with strict stereo enabled warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 Conformer generation produced nothing Skipping ZINC001142702963 1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 `1' -> `1.failed' Finished preparing ZINC001142702963 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Found failed protomers Marking ZINC001142702963 as failed `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142702963' -> `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963' Building ZINC001142703026 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703026 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/792 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@@](C)([O-])[SiH3])ccc12) `ZINC001142703026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142703026 none Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@@](C)([O-])[SiH3])ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 3, 5, 2, 3, 3, 5, 15, 15, 15, 24, 26, 26, 25, 26, 26, 2, 1, 2, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 24, 24, 26, 26, 26, 26, 26, 2, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 51, 52, 26, 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, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/793 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@](C)([O-])[SiH3])ccc12) `ZINC001142703026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142703026 none Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@](C)([O-])[SiH3])ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 4, 6, 2, 4, 4, 5, 14, 14, 14, 21, 26, 26, 21, 26, 26, 2, 1, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 5, 5, 21, 21, 26, 26, 26, 26, 26, 2, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 51, 52, 26, 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, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142703026 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 Building ZINC001142703026 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703026 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 792) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@@](C)([O-])[SiH3])ccc12) `ZINC001142703026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142703026 none Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@@](C)([O-])[SiH3])ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 3, 5, 2, 3, 3, 5, 15, 15, 15, 24, 26, 26, 25, 26, 26, 2, 1, 2, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 24, 24, 26, 26, 26, 26, 26, 2, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 51, 52, 26, 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, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 793) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@](C)([O-])[SiH3])ccc12) `ZINC001142703026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 4 28 3 32 to be deleted 33 to be deleted 34 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142703026 none Cc1cc(=O)oc2cc(NC(=O)[C@H](CC(=O)OCc3ccccc3)NC(=O)[C@](C)([O-])[SiH3])ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 4, 6, 2, 4, 4, 5, 14, 14, 14, 21, 26, 26, 21, 26, 26, 2, 1, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 6, 5, 5, 21, 21, 26, 26, 26, 26, 26, 2, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 51, 52, 26, 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, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/194367/xbs-8058088.45/working/building/ZINC001142703026 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142703026 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703026 Building ZINC001142703237 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703237 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/794 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/795 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/796 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/796' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/797 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/797' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142703237 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 Building ZINC001142703237 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703237 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 794) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 795) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 796) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 797) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142703237 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 Building ZINC001142703237 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703237 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 794) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 795) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 796) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 797) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142703237 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 Building ZINC001142703237 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703237 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 794) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 795) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 42, 42, 42, 32, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 16, 11, 16, 16, 5, 11, 11, 20, 23, 23, 21, 23, 23, 5, 1, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 48, 20, 20, 23, 23, 21, 23, 23, 5, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 240 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 796) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 797) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703237.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 36 is the cov attach 4 36 0 4 36 1 4 36 2 4 36 3 40 to be deleted 41 to be deleted 42 to be deleted natoms 78 natoms 77 natoms 76 natoms 75 names: ZINC001142703237 none CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 7, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 41, 26, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 16, 11, 16, 16, 4, 11, 11, 20, 22, 22, 21, 22, 22, 4, 1, 4, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 48, 20, 20, 22, 22, 22, 22, 22, 4, 1, 1, 1] 150 rigid atoms, others: [34, 36, 37, 38, 72, 73, 74] set([0, 1, 2, 3, 4, 5, 6, 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, 35, 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, 67, 68, 69, 70, 71]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001142703237 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001142703237 Building ZINC001143952968 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143952968 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/798 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001143952968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143952968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143952968 none C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 4, 13, 13, 4, 13, 13, 31, 32, 32, 32, 41, 41, 32, 32, 32, 32, 32, 32, 32, 13, 12, 12, 12, 1, 1, 1, 1, 1, 13, 13, 4, 31, 31, 41, 41, 41, 41, 41, 41, 41, 32, 32, 32, 13] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/799 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001143952968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143952968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143952968 none C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 3, 4, 4, 2, 1, 2, 1, 1, 1, 1, 3, 12, 12, 3, 12, 12, 30, 31, 31, 31, 40, 40, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 3, 30, 30, 40, 40, 40, 40, 40, 40, 40, 31, 31, 31, 12] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143952968 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 Building ZINC001143952968 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143952968 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 798) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001143952968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143952968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143952968 none C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 2, 1, 2, 1, 1, 1, 1, 4, 13, 13, 4, 13, 13, 31, 32, 32, 32, 41, 41, 32, 32, 32, 32, 32, 32, 32, 13, 12, 12, 12, 1, 1, 1, 1, 1, 13, 13, 4, 31, 31, 41, 41, 41, 41, 41, 41, 41, 32, 32, 32, 13] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 191 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 799) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001143952968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143952968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143952968 none C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])CC)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 3, 4, 4, 2, 1, 2, 1, 1, 1, 1, 3, 12, 12, 3, 12, 12, 30, 31, 31, 31, 40, 40, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 3, 30, 30, 40, 40, 40, 40, 40, 40, 40, 31, 31, 31, 12] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 194 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143952968 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143952968 Building ZINC001143968979 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143968979 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/800 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 23, 34, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 23, 23, 34, 34, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/801 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/802 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/802' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 24, 35, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 24, 24, 35, 35, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/803 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/803' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143968979 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 Building ZINC001143968979 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143968979 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 800) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 23, 34, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 23, 23, 34, 34, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 801) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 802) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 24, 35, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 24, 24, 35, 35, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 803) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143968979 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 Building ZINC001143968979 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143968979 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 800) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 23, 34, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 23, 23, 34, 34, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 801) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 802) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 24, 35, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 24, 24, 35, 35, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 803) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143968979 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 Building ZINC001143968979 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143968979 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 800) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 23, 34, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 23, 23, 34, 34, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 801) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 802) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 5, 5, 7, 14, 14, 14, 14, 14, 24, 35, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 14, 14, 14, 14, 24, 24, 35, 35, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 32, 33, 2, 3, 36, 4] set([5, 6, 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, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 803) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2) `ZINC001143968979.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143968979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001143968979 none CC[C@]([O-])([SiH3])C(=O)Nc1c2c(c(C(=O)N[C@H]3CC[N@@](CCCOC)CC3)cc1Cl)OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 1, 1, 16, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 21, 32, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 21, 21, 32, 32, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143968979 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143968979 Building ZINC001143972288 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972288 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/804 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(COCCN)N(C(=O)[C@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001143972288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001143972288 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 1, 6, 1, 1, 1, 3, 8, 23, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 2, 2, 1, 2, 2, 2, 17, 17, 17, 17, 17, 3, 3, 23, 23, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 2, 2, 1, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 4, 8, 9, 10, 11, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 202 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/805 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(COCCN)N(C(=O)[C@@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001143972288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001143972288 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 1, 1, 1, 3, 9, 25, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 2, 2, 1, 2, 2, 2, 16, 16, 16, 16, 16, 3, 3, 25, 25, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 2, 2, 1, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 4, 8, 9, 10, 11, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143972288 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 Building ZINC001143972288 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972288 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 804) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C(COCCN)N(C(=O)[C@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001143972288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001143972288 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 1, 6, 1, 1, 1, 3, 8, 23, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 2, 2, 1, 2, 2, 2, 17, 17, 17, 17, 17, 3, 3, 23, 23, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 2, 2, 1, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 4, 8, 9, 10, 11, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 202 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 805) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C(COCCN)N(C(=O)[C@@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl) `ZINC001143972288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001143972288 none CCOC(=O)C1=C(COCCN)N(C(=O)[C@@]([O-])([SiH3])CC)C(C)=C(C(=O)OC)[C@@H]1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 5, 1, 1, 11, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 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, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 1, 1, 1, 3, 9, 25, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 2, 2, 1, 2, 2, 2, 16, 16, 16, 16, 16, 3, 3, 25, 25, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 2, 2, 1, 2] 50 rigid atoms, others: [3, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 4, 8, 9, 10, 11, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001143972288 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001143972288 Building ZINC001144037502 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144037502 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/806 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC) `ZINC001144037502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144037502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001144037502 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 5, 12, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 1, 1, 1, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 37, 10, 10, 10, 10, 10, 9, 9, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 37, 37, 37, 37, 37] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/807 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC) `ZINC001144037502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144037502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001144037502 none CCC[C@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 5, 12, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 40, 10, 10, 10, 10, 10, 9, 9, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 96, 40, 40, 40, 40, 40] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56]) total number of confs: 223 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144037502 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 Building ZINC001144037502 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144037502 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 806) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC) `ZINC001144037502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144037502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001144037502 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 5, 12, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 1, 1, 1, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 37, 10, 10, 10, 10, 10, 9, 9, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 37, 37, 37, 37, 37] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 807) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC) `ZINC001144037502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144037502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001144037502 none CCC[C@]([O-])([SiH3])C(=O)Nc1cccc2nc3c(cc21)Cn1c-3cc2c(c1=O)COC(=O)[C@]2(O)CC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 5, 12, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 40, 10, 10, 10, 10, 10, 9, 9, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 96, 40, 40, 40, 40, 40] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56]) total number of confs: 223 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144037502 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144037502 Building ZINC001144041069 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041069 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/808 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/809 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/810 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/810' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/811 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/811' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041069 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 Building ZINC001144041069 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041069 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 808) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 809) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 810) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 811) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041069 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 Building ZINC001144041069 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041069 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 808) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 809) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 810) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 811) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041069 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 Building ZINC001144041069 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041069 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 808) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 809) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 810) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 40, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 811) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041069 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 4, 4, 4, 7, 4, 4, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 3, 4, 7, 7, 7, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041069 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041069 Building ZINC001144041070 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041070 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/812 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/813 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/814 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/814' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/815 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/815' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041070 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 Building ZINC001144041070 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041070 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 812) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 813) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 814) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 815) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041070 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 Building ZINC001144041070 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041070 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 812) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 813) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 814) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 815) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041070 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 Building ZINC001144041070 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144041070 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 812) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 813) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 814) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 13, 13, 13, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 13, 41, 41, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 815) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001144041070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144041070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001144041070 none CCC[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 5, 5, 8, 5, 5, 12, 12, 12, 41, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 12, 40, 40, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 39, 2, 3, 4, 5] set([6, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144041070 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144041070 Building ZINC001144043117 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144043117 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/816 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)cc1) `ZINC001144043117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144043117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144043117 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 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, 7, 7, 6, 6, 7, 7] dock color type numbers: [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, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 8, 8, 8, 8, 5, 11, 11, 11, 16, 19, 34, 34, 34, 19, 36, 36, 36, 49, 49, 36, 36, 49, 49, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 8, 8, 8, 33, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 413 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/817 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)cc1) `ZINC001144043117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144043117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144043117 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 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, 7, 7, 6, 6, 7, 7] dock color type numbers: [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, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 8, 8, 8, 8, 8, 6, 12, 12, 12, 15, 20, 32, 32, 32, 20, 40, 40, 40, 47, 47, 44, 45, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 36, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 336 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144043117 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 Building ZINC001144043117 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144043117 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 816) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)cc1) `ZINC001144043117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144043117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144043117 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 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, 7, 7, 6, 6, 7, 7] dock color type numbers: [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, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 8, 8, 8, 8, 5, 11, 11, 11, 16, 19, 34, 34, 34, 19, 36, 36, 36, 49, 49, 36, 36, 49, 49, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 8, 8, 8, 33, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 413 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 817) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)cc1) `ZINC001144043117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144043117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144043117 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)[C@H](O)CN(CC(C)C)S(=O)(=O)c1ccc(N)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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 5, 5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 7, 7, 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, 7, 7, 6, 6, 7, 7] dock color type numbers: [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, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 8, 8, 8, 8, 8, 6, 12, 12, 12, 15, 20, 32, 32, 32, 20, 40, 40, 40, 47, 47, 44, 45, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 36, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 336 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144043117 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144043117 Building ZINC001144045212 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045212 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/818 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC) `ZINC001144045212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144045212 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 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: [6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 25, 27, 27, 27, 25, 25, 27, 27, 27, 14, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 3, 25, 25, 27, 54, 27, 24, 24, 24] 100 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/819 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC) `ZINC001144045212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144045212 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 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: [5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 3, 28, 28, 28, 56, 28, 26, 26, 26] 100 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144045212 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 Building ZINC001144045212 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045212 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 818) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC) `ZINC001144045212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144045212 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 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: [6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 25, 27, 27, 27, 25, 25, 27, 27, 27, 14, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 3, 25, 25, 27, 54, 27, 24, 24, 24] 100 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 819) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC) `ZINC001144045212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144045212 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cc(Br)c(O)c(Br)c1)C(=O)OC 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 17, 1, 12, 1, 17, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 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: [5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 3, 28, 28, 28, 56, 28, 26, 26, 26] 100 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 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]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144045212 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144045212 Building ZINC001144899216 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899216 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/820 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899216 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 9, 9, 9, 12, 3, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 9, 27, 12, 12, 36] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 1227 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/821 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899216 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 6, 6, 6, 8, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 9, 18, 8, 8, 24] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 1551 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899216 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 Building ZINC001144899216 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899216 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 820) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899216 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 9, 9, 9, 12, 3, 3, 8, 8, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 6, 9, 27, 12, 12, 36] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 154 number of broken/clashed sets: 1227 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 821) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899216 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 6, 6, 6, 8, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 9, 18, 8, 8, 24] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 1551 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899216 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899216 Building ZINC001144899217 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899217 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/822 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899217 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 5, 5, 5, 7, 4, 4, 10, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 3, 3, 3, 3, 6, 9, 15, 7, 7, 21] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 1170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/823 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899217 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 6, 9, 4, 4, 11, 11, 11, 11, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 9, 9, 27] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 134 number of broken/clashed sets: 1800 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899217 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 Building ZINC001144899217 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899217 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 822) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899217 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 5, 5, 5, 7, 4, 4, 10, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 3, 3, 3, 3, 6, 9, 15, 7, 7, 21] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 1170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 823) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899217 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 6, 9, 4, 4, 11, 11, 11, 11, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 9, 9, 27] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 134 number of broken/clashed sets: 1800 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899217 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899217 Building ZINC001144899218 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899218 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/824 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899218 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 3, 4, 4, 4, 7, 7, 7, 10, 5, 5, 13, 13, 13, 13, 13, 13, 13, 2, 2, 5, 5, 5, 5, 5, 5, 5, 9, 12, 21, 10, 10, 30] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 155 number of broken/clashed sets: 1233 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/825 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899218 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 3, 3, 3, 4, 4, 4, 5, 5, 5, 7, 4, 4, 12, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 6, 6, 6, 9, 12, 15, 7, 7, 21] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 855 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899218 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 Building ZINC001144899218 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899218 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 824) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899218 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 3, 4, 4, 4, 7, 7, 7, 10, 5, 5, 13, 13, 13, 13, 13, 13, 13, 2, 2, 5, 5, 5, 5, 5, 5, 5, 9, 12, 21, 10, 10, 30] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 155 number of broken/clashed sets: 1233 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 825) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899218 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 3, 3, 3, 4, 4, 4, 5, 5, 5, 7, 4, 4, 12, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 6, 6, 6, 9, 12, 15, 7, 7, 21] 4050 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 855 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899218 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899218 Building ZINC001144899219 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899219 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/826 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899219 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 10, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 21, 10, 10, 30] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 1248 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/827 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899219 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 6, 6, 6, 8, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 9, 18, 8, 8, 24] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 1335 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899219 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 Building ZINC001144899219 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899219 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 826) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899219 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 10, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 21, 10, 10, 30] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 1248 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 827) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001144899219 none O=C(N(Cc1ccc2ccccc2c1)Cc1ccc2ccccc2c1)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 6, 6, 6, 8, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 9, 18, 8, 8, 24] 4050 rigid atoms, others: [0, 1, 2, 3, 14, 15, 48, 27, 25, 26, 47] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 1335 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899219 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899219 Building ZINC001144899296 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899296 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/828 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899296 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 11, 12, 12, 12, 12, 12, 4, 7, 9, 9, 18, 18, 18, 18, 18, 18, 18, 20, 20, 20, 20, 20, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 11, 11, 11, 12, 12, 12, 12, 12, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 20, 20, 20, 20, 20, 3, 3, 15, 6, 6, 18] 4050 rigid atoms, others: [32, 33, 34, 35, 25, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 36, 37, 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, 67, 68]) total number of confs: 165 number of broken/clashed sets: 2721 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/829 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899296 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 4, 6, 6, 4, 6, 6, 2, 3, 5, 5, 10, 12, 12, 10, 12, 12, 10, 13, 13, 13, 13, 13, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 6, 4, 4, 4, 6, 6, 4, 6, 6, 5, 5, 5, 5, 10, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 6, 6, 15, 6, 6, 18] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 147 number of broken/clashed sets: 2358 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899296 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 Building ZINC001144899296 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899296 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 828) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899296 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 11, 11, 12, 12, 12, 12, 12, 4, 7, 9, 9, 18, 18, 18, 18, 18, 18, 18, 20, 20, 20, 20, 20, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 11, 11, 11, 12, 12, 12, 12, 12, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 20, 20, 20, 20, 20, 3, 3, 15, 6, 6, 18] 4050 rigid atoms, others: [32, 33, 34, 35, 25, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 36, 37, 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, 67, 68]) total number of confs: 165 number of broken/clashed sets: 2721 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 829) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO) `ZINC001144899296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899296 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 4, 6, 6, 4, 6, 6, 2, 3, 5, 5, 10, 12, 12, 10, 12, 12, 10, 13, 13, 13, 13, 13, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 6, 4, 4, 4, 6, 6, 4, 6, 6, 5, 5, 5, 5, 10, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 6, 6, 15, 6, 6, 18] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 147 number of broken/clashed sets: 2358 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899296 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899296 Building ZINC001144899297 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899297 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/830 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899297 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 17, 17, 19, 19, 17, 19, 19, 3, 10, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 3, 1, 1, 1, 3, 3, 3, 4, 4, 4, 7, 7, 7, 8, 17, 17, 17, 19, 19, 17, 19, 19, 14, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 12, 21, 8, 8, 24] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 238 number of broken/clashed sets: 2502 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/831 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899297 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 4, 4, 3, 4, 4, 2, 3, 5, 5, 11, 13, 13, 11, 13, 13, 11, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 11, 3, 3, 3, 4, 4, 3, 4, 4, 5, 5, 5, 5, 11, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 6, 9, 21, 11, 11, 33] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 193 number of broken/clashed sets: 2139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899297 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 Building ZINC001144899297 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899297 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 830) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899297 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 17, 17, 19, 19, 17, 19, 19, 3, 10, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 3, 1, 1, 1, 3, 3, 3, 4, 4, 4, 7, 7, 7, 8, 17, 17, 17, 19, 19, 17, 19, 19, 14, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 12, 21, 8, 8, 24] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 238 number of broken/clashed sets: 2502 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 831) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO) `ZINC001144899297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899297 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 4, 4, 3, 4, 4, 2, 3, 5, 5, 11, 13, 13, 11, 13, 13, 11, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 11, 3, 3, 3, 4, 4, 3, 4, 4, 5, 5, 5, 5, 11, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 6, 9, 21, 11, 11, 33] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 193 number of broken/clashed sets: 2139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899297 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899297 Building ZINC001144899298 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899298 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/832 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899298 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 15, 15, 16, 16, 16, 16, 16, 4, 10, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 8, 10, 15, 15, 15, 16, 16, 16, 16, 16, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 9, 24, 10, 10, 30] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 213 number of broken/clashed sets: 2439 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/833 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899298 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 4, 6, 6, 4, 6, 6, 2, 3, 5, 5, 10, 11, 11, 10, 11, 11, 10, 13, 13, 13, 13, 13, 1, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 7, 4, 4, 4, 6, 6, 4, 6, 6, 5, 5, 5, 5, 10, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 6, 9, 21, 7, 7, 21] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 161 number of broken/clashed sets: 2169 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899298 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 Building ZINC001144899298 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899298 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 832) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899298 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 15, 15, 16, 16, 16, 16, 16, 4, 10, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 8, 8, 8, 10, 15, 15, 15, 16, 16, 16, 16, 16, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 9, 24, 10, 10, 30] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 213 number of broken/clashed sets: 2439 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 833) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO) `ZINC001144899298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899298 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 4, 4, 6, 6, 4, 6, 6, 2, 3, 5, 5, 10, 11, 11, 10, 11, 11, 10, 13, 13, 13, 13, 13, 1, 2, 1, 1, 1, 2, 2, 2, 3, 3, 3, 7, 7, 7, 7, 4, 4, 4, 6, 6, 4, 6, 6, 5, 5, 5, 5, 10, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 6, 9, 21, 7, 7, 21] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 161 number of broken/clashed sets: 2169 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899298 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899298 Building ZINC001144899299 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899299 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/834 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899299 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 16, 16, 18, 18, 16, 18, 18, 3, 10, 14, 14, 26, 28, 28, 26, 28, 28, 26, 28, 28, 28, 28, 28, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 6, 8, 16, 16, 16, 18, 18, 16, 18, 18, 14, 14, 14, 14, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 18, 8, 8, 24] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 259 number of broken/clashed sets: 1665 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/835 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899299 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 4, 4, 3, 4, 4, 2, 3, 5, 5, 11, 13, 13, 11, 13, 13, 11, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 7, 3, 3, 3, 4, 4, 3, 4, 4, 5, 5, 5, 5, 11, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 9, 9, 15, 7, 7, 21] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 157 number of broken/clashed sets: 1665 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899299 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 Building ZINC001144899299 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144899299 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 834) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144899299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899299 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [16, 10, 16, 16, 18, 18, 16, 18, 18, 3, 10, 14, 14, 26, 28, 28, 26, 28, 28, 26, 28, 28, 28, 28, 28, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 6, 8, 16, 16, 16, 18, 18, 16, 18, 18, 14, 14, 14, 14, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 18, 8, 8, 24] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 259 number of broken/clashed sets: 1665 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 835) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO) `ZINC001144899299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144899299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001144899299 none C[C@H](c1ccccc1)N(CCC(c1ccccc1)c1ccccc1)C(=O)[C@]([O-])([SiH3])[C@H](O)[C@H](O)[C@H](O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.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', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 7, 12, 5, 7, 12, 5, 7, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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, 4, 7, 7, 4, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 4 hydrogens need rotated 4050 conformations in input total number of sets (complete confs): 4050 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 4, 4, 3, 4, 4, 2, 3, 5, 5, 11, 13, 13, 11, 13, 13, 11, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 7, 3, 3, 3, 4, 4, 3, 4, 4, 5, 5, 5, 5, 11, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 9, 9, 15, 7, 7, 21] 4050 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 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, 67, 68]) total number of confs: 157 number of broken/clashed sets: 1665 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001144899299 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001144899299 Building ZINC001149775298 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149775298 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/836 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149775298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775298 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 19, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 7, 7, 5, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 3, 1, 4, 4, 1, 1, 1, 1, 7, 7, 5, 7, 7] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/837 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149775298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775298 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 7, 7, 4, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 7, 7, 4, 7, 7] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001149775298 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 Building ZINC001149775298 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149775298 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 836) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149775298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775298 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 19, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 7, 7, 5, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 3, 1, 4, 4, 1, 1, 1, 1, 7, 7, 5, 7, 7] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 837) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149775298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775298 none Cc1cccc(C)c1OC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 15, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 7, 7, 4, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 2, 1, 4, 4, 1, 1, 1, 1, 7, 7, 4, 7, 7] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001149775298 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775298 Building ZINC001149775299 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149775299 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/838 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149775299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775299 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 14, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 8, 8, 5, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 14, 3, 1, 4, 4, 1, 1, 1, 1, 8, 8, 5, 8, 8] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/839 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149775299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775299 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 17, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 7, 7, 5, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 17, 3, 1, 4, 4, 1, 1, 1, 1, 7, 7, 5, 7, 7] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001149775299 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 Building ZINC001149775299 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001149775299 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 838) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149775299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775299 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 14, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 8, 8, 5, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 14, 3, 1, 4, 4, 1, 1, 1, 1, 8, 8, 5, 8, 8] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 839) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001149775299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149775299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001149775299 none Cc1cccc(C)c1OC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 17, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 5, 7, 7, 5, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 17, 3, 1, 4, 4, 1, 1, 1, 1, 7, 7, 5, 7, 7] 50 rigid atoms, others: [48, 45, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001149775299 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001149775299 Building ZINC001150177998 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150177998 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/840 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001150177998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150177998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177998 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 15, 22, 48, 49, 49, 48, 48, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 45, 22, 22, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 210 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/841 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001150177998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150177998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177998 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 13, 18, 18, 17, 26, 48, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 13, 13, 54, 26, 26, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001150177998 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 Building ZINC001150177998 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150177998 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 840) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001150177998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150177998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177998 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 15, 22, 48, 49, 49, 48, 48, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 45, 22, 22, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 210 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 841) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001150177998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150177998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177998 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 13, 18, 18, 17, 26, 48, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 13, 13, 54, 26, 26, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 225 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001150177998 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177998 Building ZINC001150177999 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150177999 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/842 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001150177999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150177999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177999 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 13, 18, 18, 17, 26, 48, 50, 50, 48, 48, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 13, 13, 54, 26, 26, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/843 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001150177999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150177999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177999 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 15, 23, 48, 49, 49, 48, 48, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 45, 23, 23, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001150177999 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 Building ZINC001150177999 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150177999 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 842) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001150177999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150177999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177999 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 13, 18, 18, 17, 26, 48, 50, 50, 48, 48, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 13, 13, 54, 26, 26, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 843) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001150177999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150177999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001150177999 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 15, 23, 48, 49, 49, 48, 48, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 45, 23, 23, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 214 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001150177999 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150177999 Building ZINC001150439466 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150439466 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/844 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1) `ZINC001150439466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150439466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001150439466 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 3, 14, 14, 18, 18, 19, 18, 19, 18, 15, 14, 14, 7, 7, 5, 5, 5, 5, 17, 17, 5, 3, 7, 7, 18, 18, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/845 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1) `ZINC001150439466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150439466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001150439466 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 3, 15, 17, 18, 18, 18, 18, 18, 18, 17, 15, 16, 7, 7, 5, 5, 5, 5, 17, 17, 5, 3, 7, 7, 17, 18, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001150439466 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 Building ZINC001150439466 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150439466 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 844) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1) `ZINC001150439466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150439466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001150439466 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 3, 14, 14, 18, 18, 19, 18, 19, 18, 15, 14, 14, 7, 7, 5, 5, 5, 5, 17, 17, 5, 3, 7, 7, 18, 18, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 845) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1) `ZINC001150439466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150439466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001150439466 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nc3cc(F)c(F)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 3, 15, 17, 18, 18, 18, 18, 18, 18, 17, 15, 16, 7, 7, 5, 5, 5, 5, 17, 17, 5, 3, 7, 7, 17, 18, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001150439466 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001150439466 Building ZINC001151212965 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151212965 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/846 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001151212965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151212965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001151212965 none COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 19, 11, 19, 19, 11, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 19, 19, 30, 30, 30, 30, 30, 30, 30, 19, 19, 11, 11, 6, 6, 2, 1, 3, 3, 1, 1, 1, 1, 19, 19, 30, 30] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/847 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001151212965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151212965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001151212965 none COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 20, 11, 20, 20, 11, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 20, 20, 30, 30, 30, 30, 30, 30, 30, 20, 20, 11, 11, 6, 6, 2, 1, 3, 3, 1, 1, 1, 1, 20, 20, 30, 30] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001151212965 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 Building ZINC001151212965 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151212965 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 846) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001151212965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151212965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001151212965 none COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 19, 11, 19, 19, 11, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 19, 19, 30, 30, 30, 30, 30, 30, 30, 19, 19, 11, 11, 6, 6, 2, 1, 3, 3, 1, 1, 1, 1, 19, 19, 30, 30] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 847) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001151212965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151212965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001151212965 none COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 20, 11, 20, 20, 11, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 20, 20, 30, 30, 30, 30, 30, 30, 30, 20, 20, 11, 11, 6, 6, 2, 1, 3, 3, 1, 1, 1, 1, 20, 20, 30, 30] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001151212965 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001151212965 Building ZINC001152643032 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152643032 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/848 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl) `ZINC001152643032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152643032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001152643032 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 13, 22, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 22, 22, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/849 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl) `ZINC001152643032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152643032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001152643032 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 13, 22, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 22, 22, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001152643032 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 Building ZINC001152643032 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152643032 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 848) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl) `ZINC001152643032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152643032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001152643032 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 13, 22, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 22, 22, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 849) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl) `ZINC001152643032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152643032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001152643032 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCSCc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 13, 22, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 22, 22, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/194367/xbs-8058088.45/working/building/ZINC001152643032 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001152643032 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001152643032 Building ZINC001154279407 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154279407 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/850 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279407 none CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 4, 4, 15, 15, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/851 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279407 none CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 7, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 4, 4, 15, 15, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154279407 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 Building ZINC001154279407 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154279407 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 850) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279407 none CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 4, 4, 15, 15, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 851) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279407 none CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 7, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 4, 4, 15, 15, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154279407 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279407 Building ZINC001154279408 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154279408 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/852 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154279408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279408 none CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 7, 11, 11, 7, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 4, 4, 15, 15, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/853 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154279408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279408 none CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 16, 16, 16, 4, 4, 4, 7, 10, 10, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 4, 4, 16, 16, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154279408 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 Building ZINC001154279408 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154279408 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 852) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154279408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279408 none CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 7, 11, 11, 7, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 4, 4, 15, 15, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 853) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1) `ZINC001154279408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154279408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001154279408 none CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(Br)cc1 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 16, 16, 16, 4, 4, 4, 7, 10, 10, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 4, 4, 16, 16, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154279408 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154279408 Building ZINC001154519545 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154519545 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/854 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1) `ZINC001154519545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154519545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001154519545 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 3, 3, 1, 3, 9, 9, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/855 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1) `ZINC001154519545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154519545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001154519545 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 26, 1, 1, 1, 1, 3, 3, 1, 3, 9, 9, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154519545 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 Building ZINC001154519545 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154519545 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 854) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1) `ZINC001154519545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154519545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001154519545 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 3, 3, 1, 3, 9, 9, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 855) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1) `ZINC001154519545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154519545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001154519545 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cc(Br)c2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 26, 1, 1, 1, 1, 3, 3, 1, 3, 9, 9, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154519545 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154519545 Building ZINC001154748290 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154748290 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/856 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1) `ZINC001154748290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154748290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001154748290 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 24, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/857 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1) `ZINC001154748290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154748290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001154748290 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 2, 16, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154748290 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 Building ZINC001154748290 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154748290 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 856) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1) `ZINC001154748290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154748290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001154748290 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 6, 8, 24, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 857) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1) `ZINC001154748290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154748290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001154748290 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 2, 16, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001154748290 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001154748290 Building ZINC001155607753 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155607753 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/858 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1) `ZINC001155607753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155607753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001155607753 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 9, 9, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 9, 22, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/859 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1) `ZINC001155607753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155607753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001155607753 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 7, 7, 2, 2, 2, 2, 5, 5, 2, 7, 7, 7, 7, 7, 19, 19, 19, 19, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001155607753 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 Building ZINC001155607753 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155607753 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 858) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1) `ZINC001155607753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155607753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001155607753 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 9, 9, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 9, 22, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 859) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1) `ZINC001155607753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155607753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001155607753 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(Br)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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', 'Br', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 7, 7, 2, 2, 2, 2, 5, 5, 2, 7, 7, 7, 7, 7, 19, 19, 19, 19, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001155607753 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155607753 Building ZINC001155839888 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155839888 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/860 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/860' -> `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)N1CCn2c(Cc3cccc(Br)c3)nnc2C1) `ZINC001155839888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155839888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001155839888 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(Br)c3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 21, 42, 42, 41, 42, 42, 42, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 21, 21, 42, 42, 42, 42, 5, 5] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/861 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/861' -> `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)N1CCn2c(Cc3cccc(Br)c3)nnc2C1) `ZINC001155839888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155839888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001155839888 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(Br)c3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 15, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 15, 15, 36, 36, 36, 36, 3, 3] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001155839888 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 Building ZINC001155839888 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155839888 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 860) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(Br)c3)nnc2C1) `ZINC001155839888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155839888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001155839888 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(Br)c3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 21, 42, 42, 41, 42, 42, 42, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 21, 21, 42, 42, 42, 42, 5, 5] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 861) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(Br)c3)nnc2C1) `ZINC001155839888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155839888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001155839888 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(Br)c3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 15, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 15, 15, 36, 36, 36, 36, 3, 3] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001155839888 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001155839888 Building ZINC001156847431 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156847431 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/862 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156847431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847431 none O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 11, 11, 15, 25, 25, 25, 25, 25, 25, 11, 16, 16, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 15, 15, 25, 25, 25, 25, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/863 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156847431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847431 none O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 14, 14, 17, 24, 24, 24, 24, 24, 24, 14, 20, 20, 22, 22, 22, 22, 22, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 17, 17, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 123 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001156847431 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 Building ZINC001156847431 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156847431 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 862) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156847431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847431 none O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 11, 11, 15, 25, 25, 25, 25, 25, 25, 11, 16, 16, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 15, 15, 25, 25, 25, 25, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 863) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156847431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847431 none O=C(NC[C@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 14, 14, 17, 24, 24, 24, 24, 24, 24, 14, 20, 20, 22, 22, 22, 22, 22, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 17, 17, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 123 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001156847431 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847431 Building ZINC001156847432 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156847432 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/864 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156847432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847432 none O=C(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 15, 15, 17, 30, 30, 30, 30, 30, 30, 15, 18, 18, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 17, 17, 30, 30, 30, 30, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/865 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156847432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847432 none O=C(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 10, 13, 13, 18, 29, 29, 29, 29, 29, 29, 13, 17, 17, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 18, 18, 29, 29, 29, 29, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001156847432 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 Building ZINC001156847432 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156847432 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 864) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156847432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847432 none O=C(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 15, 15, 17, 30, 30, 30, 30, 30, 30, 15, 18, 18, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 17, 17, 30, 30, 30, 30, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 865) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156847432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156847432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001156847432 none O=C(NC[C@@H](Cc1cccc(F)c1)C(=O)N1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 10, 13, 13, 18, 29, 29, 29, 29, 29, 29, 13, 17, 17, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 18, 18, 29, 29, 29, 29, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001156847432 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001156847432 Building ZINC001158009084 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001158009084 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/866 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001158009084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001158009084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001158009084 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 14, 27, 14, 14, 14, 9, 2, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 2, 14, 14, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/867 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001158009084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001158009084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001158009084 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 30, 12, 30, 12, 12, 12, 8, 1, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 12, 12, 3, 1, 3, 12, 12, 12, 12] 50 rigid atoms, others: [11, 13, 15, 14] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001158009084 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 Building ZINC001158009084 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001158009084 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 866) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001158009084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001158009084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001158009084 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 14, 27, 14, 14, 14, 9, 2, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 2, 14, 14, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 867) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21) `ZINC001158009084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001158009084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001158009084 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]2CS(=O)(=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 30, 12, 30, 12, 12, 12, 8, 1, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 12, 12, 3, 1, 3, 12, 12, 12, 12] 50 rigid atoms, others: [11, 13, 15, 14] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001158009084 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001158009084 Building ZINC001159385626 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159385626 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/868 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001159385626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159385626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001159385626 none CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 16, 28, 16, 16, 10, 10, 10, 10, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 16, 10, 10, 10, 10, 4, 4, 10, 10, 10, 10, 16, 16] 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/869 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001159385626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159385626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001159385626 none CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 15, 31, 15, 15, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15, 15, 15, 9, 9, 9, 9, 3, 3, 9, 9, 9, 9, 15, 15] 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001159385626 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 Building ZINC001159385626 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159385626 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 868) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001159385626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159385626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001159385626 none CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 16, 28, 16, 16, 10, 10, 10, 10, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 16, 10, 10, 10, 10, 4, 4, 10, 10, 10, 10, 16, 16] 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 869) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001159385626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159385626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001159385626 none CC(C)(C)OC(=O)N1CC(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 15, 31, 15, 15, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15, 15, 15, 9, 9, 9, 9, 3, 3, 9, 9, 9, 9, 15, 15] 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001159385626 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001159385626 Building ZINC001160097389 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160097389 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/870 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/870' -> `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](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1) `ZINC001160097389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160097389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097389 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 6, 6, 12, 12, 12, 6, 14, 16, 34, 34, 34, 34, 34, 36, 36, 34, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 36, 36, 36, 36, 36, 36, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 125 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/871 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/871' -> `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](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1) `ZINC001160097389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160097389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097389 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 11, 17, 17, 17, 11, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 134 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160097389 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 Building ZINC001160097389 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160097389 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 870) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1) `ZINC001160097389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160097389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097389 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 6, 6, 12, 12, 12, 6, 14, 16, 34, 34, 34, 34, 34, 36, 36, 34, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 34, 34, 34, 34, 36, 36, 36, 36, 36, 36, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 125 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 871) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1) `ZINC001160097389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160097389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097389 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 11, 17, 17, 17, 11, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 134 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160097389 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097389 Building ZINC001160097400 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160097400 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/872 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1) `ZINC001160097400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160097400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097400 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 12, 12, 12, 8, 14, 16, 37, 37, 37, 37, 37, 38, 38, 37, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 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, 63, 64, 65, 66, 67]) total number of confs: 111 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/873 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1) `ZINC001160097400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160097400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097400 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 11, 11, 6, 16, 19, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 123 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160097400 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 Building ZINC001160097400 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160097400 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 872) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1) `ZINC001160097400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160097400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097400 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 12, 12, 12, 8, 14, 16, 37, 37, 37, 37, 37, 38, 38, 37, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 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, 63, 64, 65, 66, 67]) total number of confs: 111 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 873) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1) `ZINC001160097400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160097400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001160097400 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(C)C)C(=O)N1CC[C@H](N(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 11, 11, 6, 16, 19, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 123 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160097400 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160097400 Building ZINC001160334603 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160334603 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/874 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/875 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/876 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/876' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/877 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/877' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160334603 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 Building ZINC001160334603 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160334603 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 874) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 875) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 876) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 877) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160334603 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 Building ZINC001160334603 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160334603 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 874) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 875) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 876) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 877) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160334603 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 Building ZINC001160334603 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160334603 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 874) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 875) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 10, 10, 14, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 10, 10, 10, 14, 14, 21, 21, 29, 29, 29, 29, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 876) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 877) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl) `ZINC001160334603.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160334603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001160334603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCN(C)CCN2C(=O)c3ccccc3C2=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 2, 2, 6, 6, 11, 11, 15, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 6, 6, 6, 4, 4, 2, 2, 2, 6, 6, 6, 6, 11, 11, 11, 15, 15, 22, 22, 30, 30, 30, 30, 4] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160334603 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160334603 Building ZINC001160753173 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753173 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/878 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 12, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/879 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 18, 18, 18, 18, 18, 18, 3, 3, 3, 10, 10, 10, 10, 3, 3, 3, 2, 5, 5, 5, 14, 14, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/880 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/880' -> `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](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/881 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/881' -> `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](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 17, 17, 17, 17, 17, 17, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 5, 5, 5, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753173 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 Building ZINC001160753173 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753173 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 878) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 12, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 879) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 18, 18, 18, 18, 18, 18, 3, 3, 3, 10, 10, 10, 10, 3, 3, 3, 2, 5, 5, 5, 14, 14, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 880) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 881) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 17, 17, 17, 17, 17, 17, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 5, 5, 5, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753173 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 Building ZINC001160753173 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753173 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 878) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 12, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 879) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 18, 18, 18, 18, 18, 18, 3, 3, 3, 10, 10, 10, 10, 3, 3, 3, 2, 5, 5, 5, 14, 14, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 880) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 881) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 17, 17, 17, 17, 17, 17, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 5, 5, 5, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753173 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 Building ZINC001160753173 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753173 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 878) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 12, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 879) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 18, 18, 18, 18, 18, 18, 3, 3, 3, 10, 10, 10, 10, 3, 3, 3, 2, 5, 5, 5, 14, 14, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 880) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 881) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753173.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 17, 17, 17, 17, 17, 17, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 5, 5, 5, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753173 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753173 Building ZINC001160753174 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753174 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/882 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 2, 2, 2, 9, 9, 8, 9, 2, 2, 2, 3, 6, 6, 6, 12, 12, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/883 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 8, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/884 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/884' -> `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](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 6, 6, 6, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/885 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/885' -> `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](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 7, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753174 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 Building ZINC001160753174 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753174 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 882) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 2, 2, 2, 9, 9, 8, 9, 2, 2, 2, 3, 6, 6, 6, 12, 12, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 883) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 8, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 884) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 6, 6, 6, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 885) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 7, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753174 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 Building ZINC001160753174 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753174 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 882) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 2, 2, 2, 9, 9, 8, 9, 2, 2, 2, 3, 6, 6, 6, 12, 12, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 883) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 8, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 884) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 6, 6, 6, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 885) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 7, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753174 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 Building ZINC001160753174 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001160753174 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 882) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 2, 2, 2, 9, 9, 8, 9, 2, 2, 2, 3, 6, 6, 6, 12, 12, 18, 18, 18, 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, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 883) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1) `ZINC001160753174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 8, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 884) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 12, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 6, 6, 6, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 885) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1) `ZINC001160753174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001160753174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160753174 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)C[N@]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 12, 12, 12, 12, 12, 11, 3, 3, 3, 14, 14, 7, 14, 3, 3, 3, 2, 5, 5, 5, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160753174 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160753174 Building ZINC001160892939 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160892939 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/886 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/886' -> `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)N1CCc2nn(C)c(=O)cc2C1) `ZINC001160892939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160892939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160892939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nn(C)c(=O)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/887 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/887' -> `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)N1CCc2nn(C)c(=O)cc2C1) `ZINC001160892939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160892939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160892939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn(C)c(=O)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160892939 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 Building ZINC001160892939 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160892939 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 886) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nn(C)c(=O)cc2C1) `ZINC001160892939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160892939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160892939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nn(C)c(=O)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 887) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn(C)c(=O)cc2C1) `ZINC001160892939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160892939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001160892939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn(C)c(=O)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 8, 8, 5, 1, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001160892939 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001160892939 Building ZINC001161608918 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608918 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/888 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608918 none COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 4, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 8, 8, 8, 4, 4, 12, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/889 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608918 none COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 12, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 6, 12, 12, 12, 6, 6, 18, 6, 6, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 6, 6] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608918 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 Building ZINC001161608918 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608918 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 888) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608918 none COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 4, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 8, 8, 8, 4, 4, 12, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 889) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608918 none COC(=O)[C@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 12, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 6, 12, 12, 12, 6, 6, 18, 6, 6, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 6, 6] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608918 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608918 Building ZINC001161608919 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608919 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/890 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608919 none COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 5, 13, 13, 13, 5, 5, 15, 5, 5, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 5, 5] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/891 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608919 none COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 4, 9, 9, 9, 4, 4, 12, 4, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608919 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 Building ZINC001161608919 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608919 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 890) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608919 none COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 5, 13, 13, 13, 5, 5, 15, 5, 5, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 5, 5] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 891) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608919 none COC(=O)[C@@H]1C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 4, 9, 9, 9, 4, 4, 12, 4, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608919 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608919 Building ZINC001161608920 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608920 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/892 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608920 none COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 11, 11, 11, 6, 6, 18, 6, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/893 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608920 none COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 9, 9, 9, 4, 4, 12, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608920 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 Building ZINC001161608920 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608920 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 892) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608920 none COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 11, 11, 11, 6, 6, 18, 6, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 893) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608920 none COC(=O)[C@@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 9, 9, 9, 4, 4, 12, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/194367/xbs-8058088.45/working/building/ZINC001161608920 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608920 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608920 Building ZINC001161608921 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608921 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/894 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608921 none COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 3, 7, 7, 7, 3, 3, 9, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/895 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608921 none COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 9, 9, 9, 5, 5, 15, 5, 5, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 5, 5] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608921 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 Building ZINC001161608921 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161608921 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 894) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161608921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608921 none COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 3, 7, 7, 7, 3, 3, 9, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 895) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001161608921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161608921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001161608921 none COC(=O)[C@H]1C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 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, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 9, 9, 9, 5, 5, 15, 5, 5, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 5, 5] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001161608921 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001161608921 Building ZINC001180964677 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964677 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/896 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O) `ZINC001180964677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001180964677 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 37, 15, 15, 15, 15, 15, 15, 7, 1, 8, 1, 1, 1, 6, 6, 8, 8, 7, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 32, 32, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 15, 15, 15, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/897 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O) `ZINC001180964677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001180964677 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 40, 14, 14, 14, 14, 14, 14, 6, 1, 7, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 40, 40, 40, 40, 40, 40, 34, 34, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 165 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180964677 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 Building ZINC001180964677 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964677 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 896) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O) `ZINC001180964677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001180964677 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 37, 15, 15, 15, 15, 15, 15, 7, 1, 8, 1, 1, 1, 6, 6, 8, 8, 7, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 32, 32, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 8, 8, 8, 8, 8, 15, 15, 15, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 897) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O) `ZINC001180964677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001180964677 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 40, 14, 14, 14, 14, 14, 14, 6, 1, 7, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 40, 40, 40, 40, 40, 40, 34, 34, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 165 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180964677 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180964677 Building ZINC001180965289 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965289 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/898 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180965289 none O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 14, 11, 11, 12, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 4, 7, 8, 10, 11, 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, 1, 4, 4, 10, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 5, 5, 10, 10, 7, 10, 10, 4, 10, 20, 10, 10, 20, 10, 20, 5, 5, 5, 5, 10, 10, 10, 10, 10] 100 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/899 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180965289 none O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 14, 11, 11, 12, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 4, 7, 8, 10, 11, 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: [5, 1, 5, 5, 12, 12, 12, 21, 21, 21, 12, 12, 12, 12, 12, 21, 21, 21, 12, 12, 12, 12, 1, 1, 1, 5, 5, 11, 11, 7, 11, 11, 5, 12, 21, 12, 12, 21, 12, 24, 5, 5, 5, 5, 11, 11, 11, 11, 11] 100 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180965289 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 Building ZINC001180965289 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965289 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 898) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180965289 none O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 14, 11, 11, 12, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 4, 7, 8, 10, 11, 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, 1, 4, 4, 10, 10, 10, 20, 20, 20, 10, 10, 10, 10, 10, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 5, 5, 10, 10, 7, 10, 10, 4, 10, 20, 10, 10, 20, 10, 20, 5, 5, 5, 5, 10, 10, 10, 10, 10] 100 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 899) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180965289 none O=C(Nc1cc(S(=O)(=O)O)cc2cc(S(=O)(=O)O)cc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 14, 11, 11, 12, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 6, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 4, 7, 8, 10, 11, 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: [5, 1, 5, 5, 12, 12, 12, 21, 21, 21, 12, 12, 12, 12, 12, 21, 21, 21, 12, 12, 12, 12, 1, 1, 1, 5, 5, 11, 11, 7, 11, 11, 5, 12, 21, 12, 12, 21, 12, 24, 5, 5, 5, 5, 11, 11, 11, 11, 11] 100 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180965289 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965289 Building ZINC001180965631 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001180965631 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/900 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/901 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/902 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/902' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/903 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/903' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180965631 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 Building ZINC001180965631 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001180965631 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 900) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 901) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 902) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 903) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180965631 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 Building ZINC001180965631 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001180965631 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 900) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 901) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 902) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 903) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180965631 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 Building ZINC001180965631 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001180965631 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 900) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 901) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 902) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 21, 29, 29, 29, 29, 14, 14, 23, 23, 23, 23, 14, 1, 1, 1, 4, 4, 7, 7, 5, 7, 7, 14, 14, 14, 14, 14, 14, 21, 21, 29, 29, 23, 23, 14, 14, 4, 4, 4, 4, 7, 7, 6, 7, 7] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 903) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965631.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001180965631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180965631 none O=C(N1CC[C@H]2[C@H](C[C@@H](Cn3cncn3)N2c2nccs2)C1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 5, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 30, 30, 9, 9, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 17, 17, 9, 9, 6, 6, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180965631 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180965631 Building ZINC001180966155 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180966155 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/904 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180966155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180966155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180966155 none O=C(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 11, 11, 12, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 14, 14, 14, 13, 13, 13, 15, 15, 15, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 7, 7, 12, 12, 7, 12, 12, 5, 14, 13, 15, 13, 13, 13, 26, 7, 7, 7, 7, 12, 12, 12, 12, 12] 64 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/905 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180966155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180966155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180966155 none O=C(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 11, 11, 12, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 11, 11, 10, 11, 11, 7, 16, 16, 19, 16, 16, 16, 32, 6, 6, 6, 6, 11, 11, 11, 11, 11] 72 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180966155 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 Building ZINC001180966155 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180966155 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 904) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180966155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180966155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180966155 none O=C(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 11, 11, 12, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 14, 14, 14, 13, 13, 13, 15, 15, 15, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 7, 7, 12, 12, 7, 12, 12, 5, 14, 13, 15, 13, 13, 13, 26, 7, 7, 7, 7, 12, 12, 12, 12, 12] 64 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 905) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180966155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180966155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001180966155 none O=C(Nc1c(S(=O)(=O)O)cc(S(=O)(=O)O)c2cccc(O)c21)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 11, 11, 12, 1, 1, 14, 11, 11, 12, 1, 1, 1, 1, 1, 12, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 11, 11, 10, 11, 11, 7, 16, 16, 19, 16, 16, 16, 32, 6, 6, 6, 6, 11, 11, 11, 11, 11] 72 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180966155 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180966155 Building ZINC001180968541 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180968541 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/906 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180968541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001180968541 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 13, 13, 13, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 58, 33, 57, 56, 50, 51, 52, 53, 54, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/907 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180968541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180968541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001180968541 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 17, 17, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 58, 33, 57, 56, 50, 51, 52, 53, 54, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180968541 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 Building ZINC001180968541 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180968541 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 906) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180968541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001180968541 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 13, 13, 13, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 58, 33, 57, 56, 50, 51, 52, 53, 54, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 907) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180968541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180968541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001180968541 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 17, 17, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 58, 33, 57, 56, 50, 51, 52, 53, 54, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180968541 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968541 Building ZINC001180968612 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180968612 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/908 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)nc2C1) `ZINC001180968612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001180968612 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 29, 40, 29, 29, 29, 29, 29, 29, 29, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 29, 29] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/909 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])CCc3ccccc3)nc2C1) `ZINC001180968612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180968612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001180968612 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])CCc3ccccc3)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 41, 29, 41, 29, 29, 29, 29, 29, 29, 29, 28, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 29, 29] 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/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180968612 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 Building ZINC001180968612 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180968612 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 908) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)nc2C1) `ZINC001180968612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001180968612 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 29, 40, 29, 29, 29, 29, 29, 29, 29, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 29, 29] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 909) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])CCc3ccccc3)nc2C1) `ZINC001180968612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180968612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001180968612 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])CCc3ccccc3)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 41, 29, 41, 29, 29, 29, 29, 29, 29, 29, 28, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 29, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 29, 29] 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/194367/xbs-8058088.45/working/building/ZINC001180968612 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180968612 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180968612 Building ZINC001180969907 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969907 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/910 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001180969907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001180969907 none COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 4, 5, 5, 7, 7, 12, 15, 4, 1, 4, 1, 1, 1, 6, 6, 11, 11, 8, 11, 11, 4, 7, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 12, 12, 15, 15, 15, 15, 6, 6, 6, 6, 11, 11, 11, 11, 11, 10, 10, 10, 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, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/911 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001180969907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001180969907 none COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 3, 4, 4, 5, 6, 10, 13, 3, 1, 3, 1, 1, 1, 5, 5, 9, 9, 6, 9, 9, 3, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 6, 5, 5, 6, 6, 10, 10, 13, 13, 13, 13, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180969907 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 Building ZINC001180969907 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969907 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 910) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001180969907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001180969907 none COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 4, 5, 5, 7, 7, 12, 15, 4, 1, 4, 1, 1, 1, 6, 6, 11, 11, 8, 11, 11, 4, 7, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 12, 12, 15, 15, 15, 15, 6, 6, 6, 6, 11, 11, 11, 11, 11, 10, 10, 10, 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, 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: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 911) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001180969907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001180969907 none COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])CCc1ccccc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 3, 4, 4, 5, 6, 10, 13, 3, 1, 3, 1, 1, 1, 5, 5, 9, 9, 6, 9, 9, 3, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 6, 5, 5, 6, 6, 10, 10, 13, 13, 13, 13, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001180969907 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001180969907 Building ZINC001181378083 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181378083 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/912 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001181378083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181378083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001181378083 none Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 31, 31, 4, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 16, 16, 42, 42, 42, 31, 31, 34, 34, 34, 31, 31, 31, 31, 31, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 16, 42, 34, 31] 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]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/913 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001181378083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181378083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001181378083 none Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 30, 30, 4, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 16, 16, 42, 42, 42, 30, 30, 31, 31, 31, 30, 30, 30, 30, 30, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 16, 42, 31, 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]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181378083 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 Building ZINC001181378083 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181378083 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 912) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001181378083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181378083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001181378083 none Nc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 31, 31, 4, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 16, 16, 42, 42, 42, 31, 31, 34, 34, 34, 31, 31, 31, 31, 31, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 16, 42, 34, 31] 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]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 913) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1) `ZINC001181378083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181378083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001181378083 none Nc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)cc2S(=O)(=O)O)c(S(=O)(=O)O)c1 NO_LONG_NAME dock atom types: ['N.pl3', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 12, 1, 14, 11, 11, 12, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 7, 7, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 30, 30, 4, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 16, 16, 16, 42, 42, 42, 30, 30, 31, 31, 31, 30, 30, 30, 30, 30, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 16, 42, 31, 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]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181378083 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378083 Building ZINC001181378652 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181378652 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/914 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC) `ZINC001181378652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181378652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181378652 none CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 48, 34, 28, 17, 28, 17, 7, 17, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 34, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 34, 34, 34, 34, 34] 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]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/915 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC) `ZINC001181378652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181378652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181378652 none CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 45, 45, 31, 45, 31, 26, 14, 26, 14, 8, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 26, 26, 26, 26, 35, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 35, 35, 35, 35, 35] 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]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181378652 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 Building ZINC001181378652 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181378652 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 914) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC) `ZINC001181378652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181378652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181378652 none CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 48, 34, 28, 17, 28, 17, 7, 17, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 34, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 34, 34, 34, 34, 34] 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]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 915) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC) `ZINC001181378652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181378652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181378652 none CCOC(=O)CC[C@H](NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1)C(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 45, 45, 31, 45, 31, 26, 14, 26, 14, 8, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 26, 26, 26, 26, 35, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 35, 35, 35, 35, 35] 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]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181378652 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181378652 Building ZINC001181379826 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181379826 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/916 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181379826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181379826 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 5, 8, 3, 5, 5, 11, 11, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 17, 17, 22, 22, 36, 36, 36, 36, 36, 8, 11, 11, 11, 11, 11, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/917 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181379826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181379826 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 10, 10, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 5, 6, 3, 5, 5, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 25, 25, 42, 42, 42, 42, 42, 6, 12, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181379826 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 Building ZINC001181379826 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181379826 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 916) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181379826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181379826 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 5, 8, 3, 5, 5, 11, 11, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 17, 17, 22, 22, 36, 36, 36, 36, 36, 8, 11, 11, 11, 11, 11, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 917) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181379826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 31 is the cov attach 4 31 0 4 31 1 4 31 2 3 31 2 34 to be deleted 35 to be deleted 36 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001181379826 none NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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.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: [8, 1, 11, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 10, 10, 25, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 5, 6, 3, 5, 5, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 12, 25, 25, 42, 42, 42, 42, 42, 6, 12, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [32, 33, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181379826 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181379826 Building ZINC001181380175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181380175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/918 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181380175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380175 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 21, 4, 4, 4, 4, 4, 9, 10, 14, 10, 12, 4, 4, 4, 6, 6, 6, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 33, 33, 33, 33, 33, 4, 10, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/919 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181380175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380175 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 21, 5, 21, 5, 5, 5, 5, 5, 8, 8, 12, 8, 12, 5, 5, 5, 10, 10, 10, 2, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 35, 35, 35, 35, 35, 5, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181380175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 Building ZINC001181380175 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181380175 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 918) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181380175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380175 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 21, 4, 4, 4, 4, 4, 9, 10, 14, 10, 12, 4, 4, 4, 6, 6, 6, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 33, 33, 33, 33, 33, 4, 10, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 919) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181380175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380175 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 21, 5, 21, 5, 5, 5, 5, 5, 8, 8, 12, 8, 12, 5, 5, 5, 10, 10, 10, 2, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 35, 35, 35, 35, 35, 5, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181380175 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380175 Building ZINC001181380176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181380176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/920 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181380176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380176 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 3, 10, 3, 3, 3, 3, 3, 6, 9, 13, 9, 11, 3, 3, 3, 3, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 3, 9, 14, 14, 14, 14, 14, 13, 13, 13, 13, 13, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/921 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181380176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380176 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 3, 17, 3, 3, 3, 3, 3, 8, 10, 12, 10, 12, 3, 3, 3, 6, 6, 6, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 3, 10, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 6, 6, 6, 6, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [23, 21, 25, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181380176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 Building ZINC001181380176 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181380176 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 920) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181380176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380176 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 10, 3, 10, 3, 3, 3, 3, 3, 6, 9, 13, 9, 11, 3, 3, 3, 3, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 27, 3, 9, 14, 14, 14, 14, 14, 13, 13, 13, 13, 13, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 921) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1) `ZINC001181380176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181380176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001181380176 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 3, 17, 3, 3, 3, 3, 3, 8, 10, 12, 10, 12, 3, 3, 3, 6, 6, 6, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 3, 10, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 6, 6, 6, 6, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [23, 21, 25, 24, 57, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181380176 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380176 Building ZINC001181380659 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181380659 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/922 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)ccc12) `ZINC001181380659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181380659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001181380659 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 43, 17, 17, 6, 17, 3, 6, 6, 15, 17, 17, 17, 17, 17, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 17, 15, 15, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 43, 43] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/923 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)ccc12) `ZINC001181380659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181380659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001181380659 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 5, 13, 3, 5, 5, 9, 10, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 13, 9, 9, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 46, 46] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181380659 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 Building ZINC001181380659 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181380659 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 922) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)ccc12) `ZINC001181380659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181380659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001181380659 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@@]([O-])([SiH3])Cc3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 43, 17, 17, 6, 17, 3, 6, 6, 15, 17, 17, 17, 17, 17, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 17, 15, 15, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 43, 43] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 923) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)ccc12) `ZINC001181380659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181380659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001181380659 none Cc1cc(=O)oc2cc(NC(=O)[C@H](Cc3cnc[nH]3)NC(=O)[C@]([O-])([SiH3])Cc3ccccc3)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 5, 13, 3, 5, 5, 9, 10, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 13, 9, 9, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 46, 46] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181380659 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181380659 Building ZINC001181381557 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181381557 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/924 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001181381557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181381557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001181381557 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 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, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 15, 26, 30, 30, 36, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/925 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001181381557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181381557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001181381557 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 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, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 12, 12, 20, 24, 24, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 12, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181381557 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 Building ZINC001181381557 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181381557 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 924) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001181381557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181381557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001181381557 none CC(C)[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 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, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 15, 26, 30, 30, 36, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 15, 15, 15, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 925) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1) `ZINC001181381557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181381557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001181381557 none CC(C)[C@H](NC(=O)[C@]([O-])([SiH3])Cc1ccccc1)C(=O)NCCOCCOCCOCc1ccccc1 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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 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, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 12, 12, 20, 24, 24, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 12, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001181381557 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001181381557 Building ZINC001182664535 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182664535 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/926 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001182664535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182664535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182664535 none C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 7, 11, 11, 3, 1, 3, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 37, 37, 37, 37, 41, 41, 37, 37, 37, 37, 37, 37, 37, 19, 20, 20, 20, 3, 3, 3, 3, 3, 19, 19, 19, 37, 37, 41, 41, 41, 41, 41, 41, 41, 37, 37, 37, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/927 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001182664535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182664535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182664535 none C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 10, 3, 1, 3, 1, 1, 1, 3, 3, 6, 19, 19, 6, 19, 19, 42, 42, 42, 42, 45, 45, 42, 42, 42, 42, 42, 42, 42, 19, 24, 24, 24, 3, 3, 3, 3, 3, 19, 19, 10, 42, 42, 45, 45, 45, 45, 45, 45, 45, 42, 42, 42, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 255 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182664535 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 Building ZINC001182664535 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182664535 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 926) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001182664535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182664535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182664535 none C=CS(=O)(=O)N(C(=O)[C@@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 7, 11, 11, 3, 1, 3, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 37, 37, 37, 37, 41, 41, 37, 37, 37, 37, 37, 37, 37, 19, 20, 20, 20, 3, 3, 3, 3, 3, 19, 19, 19, 37, 37, 41, 41, 41, 41, 41, 41, 41, 37, 37, 37, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 927) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1) `ZINC001182664535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182664535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182664535 none C=CS(=O)(=O)N(C(=O)[C@]([O-])([SiH3])C1CC1)c1cccc(Cc2nn(C(C)C)c3ncnc(N)c23)c1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 14, 11, 11, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 5, 1, 8, 8, 5, 5, 5, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 6, 6, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 10, 3, 1, 3, 1, 1, 1, 3, 3, 6, 19, 19, 6, 19, 19, 42, 42, 42, 42, 45, 45, 42, 42, 42, 42, 42, 42, 42, 19, 24, 24, 24, 3, 3, 3, 3, 3, 19, 19, 10, 42, 42, 45, 45, 45, 45, 45, 45, 45, 42, 42, 42, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 255 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182664535 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182664535 Building ZINC001182668051 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668051 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/928 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 22, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 22, 22, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/929 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 23, 23, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/930 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/930' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/931 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/931' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182668051 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 Building ZINC001182668051 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668051 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 928) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 22, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 22, 22, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 929) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 23, 23, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 930) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 931) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182668051 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 Building ZINC001182668051 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668051 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 928) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 22, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 22, 22, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 929) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 23, 23, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 930) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 931) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182668051 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 Building ZINC001182668051 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668051 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 928) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 22, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 22, 22, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 929) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 14, 14, 14, 14, 7, 14, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 50, 50, 50, 50, 50, 33, 33, 23, 23, 14, 14, 14, 14, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 930) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 931) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1) `ZINC001182668051.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001182668051 none COCCC[N@]1CC[C@@H](NC(=O)c2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])C3CC3)c3c2OCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 10, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 22, 13, 13, 13, 13, 7, 13, 4, 3, 4, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 50, 50, 50, 50, 50, 34, 34, 22, 22, 13, 13, 13, 13, 4, 3, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [51, 49, 50, 19, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182668051 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182668051 Building ZINC001182893320 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893320 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/932 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893320 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 27, 27, 27, 27, 27, 27, 27, 27, 35, 35, 35, 44, 44, 27, 26, 8, 1, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 46, 46, 46, 42, 42, 27, 27, 27, 27, 44, 44, 44, 44, 44, 27, 27, 27, 26, 2, 2, 2, 2, 27, 27, 27, 27] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/933 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893320 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 28, 28, 28, 28, 28, 28, 28, 28, 34, 34, 34, 44, 44, 28, 28, 8, 1, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 28, 44, 44, 44, 41, 41, 28, 28, 28, 28, 44, 44, 44, 44, 44, 28, 28, 28, 28, 2, 2, 2, 2, 28, 28, 28, 28] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893320 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 Building ZINC001182893320 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893320 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 932) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893320 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 27, 27, 27, 27, 27, 27, 27, 27, 35, 35, 35, 44, 44, 27, 26, 8, 1, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 46, 46, 46, 42, 42, 27, 27, 27, 27, 44, 44, 44, 44, 44, 27, 27, 27, 26, 2, 2, 2, 2, 27, 27, 27, 27] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 933) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893320 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 28, 28, 28, 28, 28, 28, 28, 28, 34, 34, 34, 44, 44, 28, 28, 8, 1, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 28, 44, 44, 44, 41, 41, 28, 28, 28, 28, 44, 44, 44, 44, 44, 28, 28, 28, 28, 2, 2, 2, 2, 28, 28, 28, 28] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893320 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893320 Building ZINC001182893322 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893322 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/934 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893322 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 34, 34, 34, 41, 41, 23, 23, 9, 1, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 44, 44, 44, 44, 44, 23, 23, 23, 23, 41, 41, 41, 41, 41, 23, 23, 23, 23, 2, 2, 2, 2, 23, 23, 23, 23] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/935 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893322 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 42, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 33, 42, 42, 21, 21, 8, 1, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 21, 21, 43, 43, 43, 42, 42, 21, 21, 21, 21, 42, 42, 42, 42, 42, 21, 21, 21, 21, 2, 2, 2, 2, 21, 21, 21, 21] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893322 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 Building ZINC001182893322 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893322 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 934) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893322 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 34, 34, 34, 41, 41, 23, 23, 9, 1, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 44, 44, 44, 44, 44, 23, 23, 23, 23, 41, 41, 41, 41, 41, 23, 23, 23, 23, 2, 2, 2, 2, 23, 23, 23, 23] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 935) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182893322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182893322 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 42, 21, 21, 21, 21, 21, 21, 21, 21, 33, 33, 33, 42, 42, 21, 21, 8, 1, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 21, 21, 43, 43, 43, 42, 42, 21, 21, 21, 21, 42, 42, 42, 42, 42, 21, 21, 21, 21, 2, 2, 2, 2, 21, 21, 21, 21] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893322 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893322 Building ZINC001182893345 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893345 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/936 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182893345 none O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 37, 50, 50, 50, 50, 50, 50, 12, 12, 12, 9, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 33, 51, 52, 53, 54, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/937 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182893345 none O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 38, 50, 50, 50, 50, 50, 50, 13, 13, 13, 11, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 33, 51, 52, 53, 54, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893345 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 Building ZINC001182893345 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893345 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 936) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182893345 none O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 37, 50, 50, 50, 50, 50, 50, 12, 12, 12, 9, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 33, 51, 52, 53, 54, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 937) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182893345 none O=C(N1C[C@H]2C[C@H]3[C@@](CN(CCc4ccccc4)S3(=O)=O)(C1)O2)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 38, 50, 50, 50, 50, 50, 50, 13, 13, 13, 11, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 33, 51, 52, 53, 54, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893345 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893345 Building ZINC001182893848 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893848 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/938 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001182893848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182893848 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 25, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 18, 23, 34, 50, 50, 50, 50, 50, 23, 23, 20, 23, 23, 23, 23, 23, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/939 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001182893848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182893848 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 17, 20, 33, 50, 50, 50, 50, 50, 20, 20, 18, 20, 20, 20, 20, 20, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893848 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 Building ZINC001182893848 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893848 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 938) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001182893848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182893848 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 25, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 18, 23, 34, 50, 50, 50, 50, 50, 23, 23, 20, 23, 23, 23, 23, 23, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 939) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001182893848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182893848 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 17, 20, 33, 50, 50, 50, 50, 50, 20, 20, 18, 20, 20, 20, 20, 20, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893848 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893848 Building ZINC001182893849 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893849 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/940 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O) `ZINC001182893849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182893849 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 34, 49, 10, 10, 10, 10, 10, 10, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 10, 50, 50, 50, 50, 50, 50, 34, 34, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 199 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/941 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O) `ZINC001182893849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182893849 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 36, 49, 11, 11, 11, 11, 11, 11, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 11, 11, 11, 13, 13, 11, 13, 13, 11, 11, 50, 50, 50, 50, 50, 50, 36, 36, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 11, 11, 13, 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, 55, 56, 57, 58]) total number of confs: 196 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893849 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 Building ZINC001182893849 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893849 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 940) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O) `ZINC001182893849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182893849 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 34, 49, 10, 10, 10, 10, 10, 10, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 10, 50, 50, 50, 50, 50, 50, 34, 34, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 10, 10, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 199 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 941) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O) `ZINC001182893849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182893849 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 36, 49, 11, 11, 11, 11, 11, 11, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 11, 11, 11, 13, 13, 11, 13, 13, 11, 11, 50, 50, 50, 50, 50, 50, 36, 36, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 11, 11, 13, 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, 55, 56, 57, 58]) total number of confs: 196 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182893849 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182893849 Building ZINC001182895842 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182895842 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/942 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1) `ZINC001182895842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182895842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001182895842 none O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 6, 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, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 41, 50, 50, 50, 50, 41, 23, 23, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/943 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1) `ZINC001182895842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182895842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001182895842 none O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 6, 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, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 42, 50, 50, 50, 50, 42, 24, 24, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182895842 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 Building ZINC001182895842 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182895842 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 942) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1) `ZINC001182895842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182895842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001182895842 none O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 6, 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, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 41, 50, 50, 50, 50, 41, 23, 23, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 943) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1) `ZINC001182895842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182895842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001182895842 none O=C(NCc1cc(=O)n2c(n1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', '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', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 6, 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, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 42, 50, 50, 50, 50, 42, 24, 24, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182895842 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182895842 Building ZINC001182896369 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896369 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/944 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001182896369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001182896369 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 26, 12, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 25, 25, 25, 36, 36, 36, 36, 36, 36, 26, 26, 26, 31, 26, 27, 27, 27, 26, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 31, 31, 31] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/945 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001182896369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001182896369 none COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 12, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 25, 25, 25, 35, 35, 25, 26, 35, 35, 27, 27, 27, 30, 27, 28, 28, 28, 27, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 30, 30, 30] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182896369 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 Building ZINC001182896369 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896369 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 944) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001182896369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001182896369 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 26, 12, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 25, 25, 25, 36, 36, 36, 36, 36, 36, 26, 26, 26, 31, 26, 27, 27, 27, 26, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 31, 31, 31] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 945) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001182896369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001182896369 none COc1cc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 12, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 25, 25, 25, 35, 35, 25, 26, 35, 35, 27, 27, 27, 30, 27, 28, 28, 28, 27, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 30, 30, 30] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182896369 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896369 Building ZINC001182896562 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896562 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/946 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001182896562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001182896562 none COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', '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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 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: [24, 24, 24, 24, 24, 24, 20, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 46, 46, 46, 49, 49, 46, 48, 49, 49, 24, 24, 35, 24, 24, 24, 24, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 35, 35, 35] 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: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/947 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncnc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001182896562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001182896562 none COc1ncnc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', '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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 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: [23, 23, 23, 23, 23, 23, 19, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 44, 44, 44, 48, 48, 47, 47, 48, 48, 23, 23, 32, 23, 23, 23, 23, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182896562 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 Building ZINC001182896562 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896562 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 946) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001182896562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001182896562 none COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', '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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 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: [24, 24, 24, 24, 24, 24, 20, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 46, 46, 46, 49, 49, 46, 48, 49, 49, 24, 24, 35, 24, 24, 24, 24, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 35, 35, 35] 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: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 947) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ncnc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001182896562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001182896562 none COc1ncnc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', '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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 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: [23, 23, 23, 23, 23, 23, 19, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 44, 44, 44, 48, 48, 47, 47, 48, 48, 23, 23, 32, 23, 23, 23, 23, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001182896562 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001182896562 Building ZINC001183096310 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096310 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/948 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1) `ZINC001183096310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183096310 none CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1 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.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 28, 21, 28, 21, 21, 21, 21, 15, 6, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 21, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 9, 9, 2, 2, 2, 5, 5, 5, 5, 5, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/949 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1) `ZINC001183096310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183096310 none CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1 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.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 28, 20, 28, 20, 20, 20, 20, 14, 7, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 20, 20, 9, 9, 3, 2, 2, 4, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096310 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 Building ZINC001183096310 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096310 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 948) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1) `ZINC001183096310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183096310 none CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1 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.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 28, 21, 28, 21, 21, 21, 21, 15, 6, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 21, 21, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 9, 9, 2, 2, 2, 5, 5, 5, 5, 5, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 949) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1) `ZINC001183096310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183096310 none CC(C)(C)OC(=O)N1CCCn2c(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nnc2C1 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.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 28, 20, 28, 20, 20, 20, 20, 14, 7, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 20, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 20, 20, 9, 9, 3, 2, 2, 4, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096310 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096310 Building ZINC001183096540 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096540 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/950 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183096540 none O=C(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 14, 14, 14, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/951 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183096540 none O=C(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 18, 18, 18, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096540 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 Building ZINC001183096540 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096540 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 950) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183096540 none O=C(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 14, 14, 14, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 951) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183096540 none O=C(N1c2ccccc2CN(C2CCNCC2)S1(=O)=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 18, 18, 18, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096540 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096540 Building ZINC001183096543 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096543 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/952 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1) `ZINC001183096543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183096543 none O=C(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1 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', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 16, 23, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 5, 16, 16, 23, 23, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7, 7, 7, 2, 2, 2, 2] 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, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/953 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1) `ZINC001183096543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183096543 none O=C(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1 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', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 23, 30, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 8, 23, 23, 30, 30, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096543 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 Building ZINC001183096543 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096543 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 952) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1) `ZINC001183096543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183096543 none O=C(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1 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', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 16, 23, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 5, 16, 16, 23, 23, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7, 7, 7, 2, 2, 2, 2] 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, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 953) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1) `ZINC001183096543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183096543 none O=C(NCCc1ccccn1)[C@@H]1CO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2C1 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', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 23, 30, 37, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 8, 23, 23, 30, 30, 37, 37, 37, 37, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096543 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096543 Building ZINC001183096566 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096566 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/954 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096566 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 18, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 8, 1, 7, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 27, 27, 27, 27, 27, 16, 16, 16, 10, 10, 8, 8, 17, 17, 17, 17, 17, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/955 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096566 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 23, 23, 23, 23, 23, 14, 14, 14, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096566 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 Building ZINC001183096566 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096566 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 954) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096566 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 18, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 8, 1, 7, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 27, 27, 27, 27, 27, 16, 16, 16, 10, 10, 8, 8, 17, 17, 17, 17, 17, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 955) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096566 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 23, 23, 23, 23, 23, 14, 14, 14, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096566 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096566 Building ZINC001183096569 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096569 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/956 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096569 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 12, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 20, 20, 20, 20, 20, 11, 11, 11, 8, 8, 7, 7, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/957 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096569 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 17, 19, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 27, 27, 27, 27, 27, 17, 17, 17, 10, 10, 8, 8, 16, 16, 16, 16, 16, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096569 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 Building ZINC001183096569 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096569 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 956) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096569 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 12, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 20, 20, 20, 20, 20, 11, 11, 11, 8, 8, 7, 7, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 957) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1) `ZINC001183096569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096569 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 17, 19, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 27, 27, 27, 27, 27, 17, 17, 17, 10, 10, 8, 8, 16, 16, 16, 16, 16, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096569 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096569 Building ZINC001183096576 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096576 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/958 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096576 none O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 45, 45, 45, 45, 45, 45, 45, 10, 10, 10, 10, 10, 7, 4, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 22, 45, 45, 45, 45, 45, 45, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/959 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096576 none O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 26, 49, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 10, 8, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 26, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096576 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 Building ZINC001183096576 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096576 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 958) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096576 none O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 45, 45, 45, 45, 45, 45, 45, 10, 10, 10, 10, 10, 7, 4, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 22, 45, 45, 45, 45, 45, 45, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 959) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096576 none O=C(NCc1ccc(F)cc1)C1=NO[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 26, 26, 49, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 10, 8, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 26, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096576 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096576 Building ZINC001183096580 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096580 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/960 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096580 none O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 29, 29, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 12, 3, 1, 5, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 29, 45, 45, 45, 45, 45, 45, 13, 13, 10, 13, 4, 4, 5, 5, 5, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/961 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096580 none O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 21, 47, 47, 47, 47, 47, 47, 47, 9, 9, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 21, 47, 47, 47, 47, 47, 47, 9, 9, 6, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096580 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 Building ZINC001183096580 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096580 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 960) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096580 none O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 29, 29, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 12, 3, 1, 5, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 29, 45, 45, 45, 45, 45, 45, 13, 13, 10, 13, 4, 4, 5, 5, 5, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 961) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183096580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096580 none O=C(NCc1ccc(F)cc1)C1=NO[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 21, 47, 47, 47, 47, 47, 47, 47, 9, 9, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 21, 47, 47, 47, 47, 47, 47, 9, 9, 6, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096580 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096580 Building ZINC001183096596 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096596 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/962 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183096596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096596 none O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 29, 37, 48, 48, 48, 48, 7, 7, 7, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 10, 29, 29, 37, 37, 48, 48, 48, 7, 7, 7, 7, 7, 7, 5, 5, 8, 8, 8, 8, 8, 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/963 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183096596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096596 none O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 25, 25, 36, 36, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096596 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 Building ZINC001183096596 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096596 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 962) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183096596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096596 none O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 29, 37, 48, 48, 48, 48, 7, 7, 7, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 10, 29, 29, 37, 37, 48, 48, 48, 7, 7, 7, 7, 7, 7, 5, 5, 8, 8, 8, 8, 8, 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 963) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183096596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183096596 none O=C(NCCc1cccs1)[C@]12COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 25, 25, 36, 36, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096596 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096596 Building ZINC001183096633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/964 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096633 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 8, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 24, 24, 10, 10, 10, 10, 10, 6, 6, 11, 11, 11, 11, 11, 10, 10, 28, 28] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/965 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096633 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 30, 30, 25, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 25, 25, 10, 10, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 10, 10, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 Building ZINC001183096633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 964) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096633 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 8, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 24, 24, 10, 10, 10, 10, 10, 6, 6, 11, 11, 11, 11, 11, 10, 10, 28, 28] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 965) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096633 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 30, 30, 25, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 25, 25, 10, 10, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 10, 10, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096633 Building ZINC001183096634 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096634 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/966 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096634 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 25, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 25, 25, 10, 10, 10, 10, 10, 7, 7, 10, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/967 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096634 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 8, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 24, 24, 10, 10, 10, 10, 10, 7, 7, 13, 13, 13, 13, 13, 10, 10, 27, 27] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096634 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 Building ZINC001183096634 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096634 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 966) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096634 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 25, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 25, 25, 10, 10, 10, 10, 10, 7, 7, 10, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 967) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1) `ZINC001183096634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096634 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.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, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 8, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 24, 24, 10, 10, 10, 10, 10, 7, 7, 13, 13, 13, 13, 13, 10, 10, 27, 27] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096634 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096634 Building ZINC001183096918 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096918 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/968 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)n1) `ZINC001183096918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096918 none Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)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.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 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] 0 hydrogens 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, 26, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 10, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 26, 26, 10, 10, 10, 10, 10, 10, 7, 7, 8, 8, 8, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/969 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)n1) `ZINC001183096918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096918 none Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)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.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 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] 0 hydrogens 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, 21, 8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 8, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 21, 21, 8, 8, 8, 8, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096918 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 Building ZINC001183096918 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096918 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 968) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)n1) `ZINC001183096918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096918 none Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)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.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 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] 0 hydrogens 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, 26, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 10, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 26, 26, 10, 10, 10, 10, 10, 10, 7, 7, 8, 8, 8, 8, 8, 10, 10, 10, 10] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 969) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)n1) `ZINC001183096918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096918 none Cc1cccc(CN2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])Cc4c[nH]c5ccccc45)CC[C@H]3C2=O)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.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 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] 0 hydrogens 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, 21, 8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 8, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 21, 21, 8, 8, 8, 8, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096918 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096918 Building ZINC001183096983 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096983 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/970 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1) `ZINC001183096983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096983 none O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1 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', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 25, 36, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 11, 25, 25, 36, 36, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 6, 6, 6, 3, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/971 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1) `ZINC001183096983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096983 none O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1 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', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 7, 18, 18, 27, 33, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 33, 33, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 153 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096983 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 Building ZINC001183096983 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096983 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 970) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1) `ZINC001183096983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096983 none O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1 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', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 25, 36, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 11, 25, 25, 36, 36, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 6, 6, 6, 3, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 971) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1) `ZINC001183096983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183096983 none O=C(NCCc1ccccn1)[C@H]1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]2O1 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', 'N.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 7, 18, 18, 27, 33, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 33, 33, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 153 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183096983 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183096983 Building ZINC001183097011 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097011 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/972 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097011 none O=C(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 25, 12, 12, 12, 12, 12, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 12, 12, 12, 12, 7, 7, 14, 14, 14, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/973 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097011 none O=C(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 10, 10, 10, 10, 10, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 10, 10, 10, 10, 6, 6, 11, 11, 11, 11, 11] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097011 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 Building ZINC001183097011 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097011 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 972) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097011 none O=C(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 25, 12, 12, 12, 12, 12, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 12, 12, 12, 12, 7, 7, 14, 14, 14, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 973) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097011 none O=C(N1CCOC[C@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 10, 10, 10, 10, 10, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 10, 10, 10, 10, 6, 6, 11, 11, 11, 11, 11] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097011 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097011 Building ZINC001183097012 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097012 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/974 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097012 none O=C(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 7, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 7, 7, 7, 7, 6, 6, 13, 13, 13, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/975 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097012 none O=C(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 6, 6, 6, 6, 6, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 9, 9, 15, 15, 15, 15, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097012 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 Building ZINC001183097012 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097012 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 974) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097012 none O=C(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 7, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 7, 7, 7, 7, 6, 6, 13, 13, 13, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 975) grep: /scratch/xiaobo/194367/xbs-8058088.45/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(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183097012 none O=C(N1CCOC[C@@]2(CN(c3ccsc3)C(=O)CO2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 6, 6, 6, 6, 6, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 6, 9, 9, 15, 15, 15, 15, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097012 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097012 Building ZINC001183097386 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097386 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/976 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097386 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 14, 14, 8, 8, 3, 1, 5, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 15, 15, 15, 14, 14, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 114 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/977 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097386 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 16, 16, 8, 8, 3, 2, 5, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 16, 16, 16, 14, 14, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 130 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097386 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 Building ZINC001183097386 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097386 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 976) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097386 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 14, 14, 8, 8, 3, 1, 5, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 15, 15, 15, 14, 14, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 114 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 977) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097386 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 16, 16, 8, 8, 3, 2, 5, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 16, 16, 16, 14, 14, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 130 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097386 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097386 Building ZINC001183097390 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097390 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/978 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097390 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 18, 18, 7, 7, 4, 1, 6, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 18, 18, 18, 14, 14, 7, 7, 7, 7, 18, 18, 18, 18, 18, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 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, 63]) total number of confs: 138 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/979 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097390 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 21, 21, 10, 10, 5, 1, 7, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 21, 21, 21, 21, 21, 10, 10, 10, 10, 8, 8, 18, 18, 18, 18, 18, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097390 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 Building ZINC001183097390 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097390 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 978) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097390 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 18, 18, 7, 7, 4, 1, 6, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 18, 18, 18, 14, 14, 7, 7, 7, 7, 18, 18, 18, 18, 18, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 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, 63]) total number of confs: 138 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 979) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183097390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097390 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 21, 21, 10, 10, 5, 1, 7, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 25, 25, 25, 20, 20, 10, 10, 10, 10, 21, 21, 21, 21, 21, 10, 10, 10, 10, 8, 8, 18, 18, 18, 18, 18, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097390 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097390 Building ZINC001183097448 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097448 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/980 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1) `ZINC001183097448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001183097448 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 26, 10, 26, 26, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 31, 31, 31, 31, 31, 31, 31, 10, 4, 4, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 4, 4, 4, 4, 31, 31] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 131 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/981 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1) `ZINC001183097448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001183097448 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 33, 31, 11, 31, 31, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 33, 33, 33, 33, 33, 33, 33, 11, 4, 4, 4, 4, 4, 7, 7, 10, 10, 10, 10, 10, 4, 4, 4, 4, 33, 33] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097448 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 Building ZINC001183097448 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097448 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 980) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1) `ZINC001183097448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001183097448 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 26, 10, 26, 26, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 31, 31, 31, 31, 31, 31, 31, 10, 4, 4, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 4, 4, 4, 4, 31, 31] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 131 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 981) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1) `ZINC001183097448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001183097448 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 33, 31, 11, 31, 31, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 33, 33, 33, 33, 33, 33, 33, 11, 4, 4, 4, 4, 4, 7, 7, 10, 10, 10, 10, 10, 4, 4, 4, 4, 33, 33] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097448 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097448 Building ZINC001183097604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/982 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097604 none O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 33, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 14, 33, 33, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 5, 5] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/983 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097604 none O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 26, 32, 32, 26, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 12, 26, 26, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 7, 7, 7, 7, 7, 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, 57, 58]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 Building ZINC001183097604 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097604 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 982) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097604 none O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 5, 14, 14, 33, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 14, 33, 33, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 7, 7, 7, 7, 7, 5, 5] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 983) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097604 none O=C(NCc1ccncc1)C1=NO[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 26, 32, 32, 26, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 12, 26, 26, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 7, 7, 7, 7, 7, 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, 57, 58]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097604 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097604 Building ZINC001183097633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/984 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097633 none O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 28, 31, 31, 30, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 10, 28, 28, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 6, 6, 6, 6, 6, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 126 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/985 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097633 none O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 13, 13, 32, 33, 33, 32, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 13, 32, 32, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 7, 7, 7, 7, 7, 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, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 Building ZINC001183097633 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097633 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 984) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097633 none O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 28, 31, 31, 30, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 10, 28, 28, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 6, 6, 6, 6, 6, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 126 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 985) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2) `ZINC001183097633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097633 none O=C(NCc1ccncc1)C1=NO[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)C2 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.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 13, 13, 32, 33, 33, 32, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 13, 32, 32, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 7, 7, 7, 7, 7, 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, 57, 58]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097633 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097633 Building ZINC001183097672 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097672 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/986 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097672 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 1 conformations in input total number of sets (complete confs): 1 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 1 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 55, 56, 57, 58, 59] set([]) total number of confs: 1 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/987 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097672 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 7, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 5, 2, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 9, 9, 9, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 7, 7, 5, 5, 9, 9, 9, 9, 9, 7, 7] 18 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]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097672 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 Building ZINC001183097672 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097672 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 986) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097672 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 1 conformations in input total number of sets (complete confs): 1 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 1 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 55, 56, 57, 58, 59] set([]) total number of confs: 1 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 987) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097672 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 7, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 5, 2, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 9, 9, 9, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 7, 7, 5, 5, 9, 9, 9, 9, 9, 7, 7] 18 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]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097672 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097672 Building ZINC001183097673 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097673 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/988 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097673 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 6, 1, 6, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 8, 8, 9, 9, 21, 21, 21, 21, 21, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/989 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097673 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 22, 22, 22, 22, 22, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097673 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 Building ZINC001183097673 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097673 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 988) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097673 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 6, 1, 6, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 8, 8, 9, 9, 21, 21, 21, 21, 21, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 989) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12) `ZINC001183097673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097673 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 22, 22, 22, 22, 22, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097673 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097673 Building ZINC001183097674 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097674 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/990 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097674 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 15, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 20, 20, 20, 20, 20, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/991 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097674 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 8, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 8, 6, 1, 6, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 8, 8, 8, 9, 9, 21, 21, 21, 21, 21, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097674 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 Building ZINC001183097674 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097674 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 990) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097674 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 15, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 20, 20, 20, 20, 20, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 991) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097674 none CS(=O)(=O)N1CC[C@@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 12, 12, 8, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 8, 6, 1, 6, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 8, 8, 8, 9, 9, 21, 21, 21, 21, 21, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097674 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097674 Building ZINC001183097677 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097677 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/992 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097677 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 9, 9, 7, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 5, 2, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 9, 9, 9, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 7, 7, 5, 5, 9, 9, 9, 9, 9, 7, 7] 23 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]) total number of confs: 54 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/993 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097677 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58, 59] set([54, 57, 55, 56, 51, 52, 53, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097677 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 Building ZINC001183097677 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097677 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 992) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097677 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 9, 9, 7, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 5, 2, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 9, 9, 9, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 7, 7, 7, 5, 5, 9, 9, 9, 9, 9, 7, 7] 23 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]) total number of confs: 54 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 993) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12) `ZINC001183097677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183097677 none CS(=O)(=O)N1CC[C@]2(c3ccccc3)CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 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] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58, 59] set([54, 57, 55, 56, 51, 52, 53, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097677 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097677 Building ZINC001183097784 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097784 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/994 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1) `ZINC001183097784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097784 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 29, 26, 26, 26, 26, 26, 26, 26, 23, 8, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 26, 8, 8, 2, 2, 2, 5, 5, 5, 5, 5, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/995 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1) `ZINC001183097784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097784 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 29, 26, 26, 26, 26, 26, 26, 26, 23, 8, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 26, 8, 8, 2, 2, 2, 5, 5, 5, 5, 5, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097784 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 Building ZINC001183097784 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097784 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 994) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1) `ZINC001183097784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097784 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 29, 26, 26, 26, 26, 26, 26, 26, 23, 8, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 26, 8, 8, 2, 2, 2, 5, 5, 5, 5, 5, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 995) grep: /scratch/xiaobo/194367/xbs-8058088.45/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: CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1) `ZINC001183097784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183097784 none CC(C)(C)OC(=O)N1CCCn2c(=O)cc(CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)nc2C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 29, 26, 26, 26, 26, 26, 26, 26, 23, 8, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 26, 8, 8, 2, 2, 2, 5, 5, 5, 5, 5, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097784 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/0.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097784 Building ZINC001183097992 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097992 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/996 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/997 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/998 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/998' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/999 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/999' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097992 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 Building ZINC001183097992 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097992 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 996) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 997) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 998) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 999) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097992 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 Building ZINC001183097992 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097992 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 996) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 997) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 998) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 999) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097992 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 Building ZINC001183097992 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097992 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 996) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `1' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 1 (index: 997) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `2' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 2 (index: 998) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 21, 20, 23, 23, 20, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 20, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 mkdir: created directory `3' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 3 (index: 999) grep: /scratch/xiaobo/194367/xbs-8058088.45/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097992.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097992 none O=C(N1CCC[C@@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 22, 22, 16, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 16, 16, 9, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097992 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 2: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/2.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/0.* 3: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/3.* 1: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992/1.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097992 Building ZINC001183097993 mkdir: created directory `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001183097993 mkdir: created directory `0' /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993/0 /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/194367/xbs-8058088.45/working/3D/1000 `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 1, 1, 15, 1, 8, 5, 5, 12, 5, 1, 1, 8, 6, 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: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 13, 13, 11, 13, 13, 13, 13, 13, 13, 17, 17, 13, 14, 17, 17, 13, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 7, 7, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993 /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Finished preparing ZINC001183097993 Recording results /scratch/xiaobo/194367/xbs-8058088.45/working /scratch/xiaobo/194367/xbs-8058088.45 Appending to /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.* 0: /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993/0.* Removing working files in /scratch/xiaobo/194367/xbs-8058088.45/working/building/ZINC001183097993 /scratch/xiaobo/194367/xbs-8058088.45 Compressing combined databse files /scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/194367/xbs-8058088.45/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/194367/xbs-8058088.45/working/3D/1001' removed directory: `/scratch/xiaobo/194367/xbs-8058088.45/working/3D' `/scratch/xiaobo/194367/xbs-8058088.45/working/protonate' -> `/scratch/xiaobo/194367/xbs-8058088.45/archive' `/scratch/xiaobo/194367/xbs-8058088.45/working/input-smiles.ism' -> `/scratch/xiaobo/194367/xbs-8058088.45/archive/input-smiles.ism' rmdir: removing directory, `/scratch/xiaobo/194367/xbs-8058088.45/working/building' rmdir: removing directory, `/scratch/xiaobo/194367/xbs-8058088.45/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/194367/xbs-8058088.45' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs' `/scratch/xiaobo/194367/xbs-8058088.45/failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/failure-reason' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp.in-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/fort.19' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/0.db2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp.o-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/fort.20' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/output.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp.o-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp.in-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.mol2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/0.mol2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/outputwat.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/output.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/name.txt' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/fort.12' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.1.db2in.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/output.1.db2in.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/ZINC001142702963.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/ZINC001142702963.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp-working.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/0.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/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/xbs/failed/ZINC001142702963/0/output.1.db2in.mol2.db2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/fort.21' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/0.mol2.original' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/temp.ZmatMOPAC' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/0/outputhex.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/failure-reason' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp.in-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/fort.19' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/0.db2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp.o-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/fort.20' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/output.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp.o-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp.in-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.mol2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/0.mol2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/outputwat.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/output.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/name.txt' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/fort.12' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.1.db2in.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/output.1.db2in.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/ZINC001142702963.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/ZINC001142702963.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp-working.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/0.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/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/xbs/failed/ZINC001142702963/ZINC001142702963/0/output.1.db2in.mol2.db2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/fort.21' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/0.mol2.original' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/temp.ZmatMOPAC' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/0/outputhex.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.in-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.19' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.o-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/failure-reason' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.20' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/1.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/1.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/output.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/output.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.o-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.in-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/outputwat.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/output.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/output.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/name.txt' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.12' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/ZINC001142702963.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/ZINC001142702963.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp-working.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.21' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.ZmatMOPAC' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/outputhex.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/1.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/1.failed/1.mol2.original' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963.ism' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/input.ism' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963-numbered.ism' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp.in-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/fort.19' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp.o-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/failure-reason' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/fort.20' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/1.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/1.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/output.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/output.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp.o-hex' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp.in-wat' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/outputwat.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/output.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/output.solv' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/name.txt' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/fort.12' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/ZINC001142702963.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/ZINC001142702963.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp-working.mol2' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/fort.21' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/temp.ZmatMOPAC' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/outputhex.log' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/1.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/1.failed/1.mol2.original' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963.ism' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/input.ism' `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/failed/ZINC001142702963/ZINC001142702963-numbered.ism' `/scratch/xiaobo/194367/xbs-8058088.45/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/finished' `/scratch/xiaobo/194367/xbs-8058088.45/finished/xbs.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/finished/xbs.db2.gz' `/scratch/xiaobo/194367/xbs-8058088.45/archive' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/archive' `/scratch/xiaobo/194367/xbs-8058088.45/archive/xbs-protomers-expanded.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/archive/xbs-protomers-expanded.ism' `/scratch/xiaobo/194367/xbs-8058088.45/archive/input-smiles.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/archive/input-smiles.ism' `/scratch/xiaobo/194367/xbs-8058088.45/archive/xbs-protonated-manual.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/archive/xbs-protonated-manual.ism' `/scratch/xiaobo/194367/xbs-8058088.45/archive/xbs-protomers.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbs/archive/xbs-protomers.ism' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/failure-reason' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.in-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.19' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.db2.gz' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.o-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.20' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.o-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.in-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.mol2.gz' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/outputwat.log' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/name.txt' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.12' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.1.db2in.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/ZINC001142702963.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp-working.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/output.1.db2in.mol2.db2.gz' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/fort.21' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/0.mol2.original' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/temp.ZmatMOPAC' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0/outputhex.log' removed directory: `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/0' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/failure-reason' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.in-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.19' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.db2.gz' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.o-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.20' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.o-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.in-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.mol2.gz' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/outputwat.log' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/name.txt' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.12' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.1.db2in.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/ZINC001142702963.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp-working.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/output.1.db2in.mol2.db2.gz' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/fort.21' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/0.mol2.original' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/temp.ZmatMOPAC' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0/outputhex.log' removed directory: `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/0' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.in-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.19' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.o-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/failure-reason' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.20' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/1.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/output.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.o-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.in-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/outputwat.log' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/output.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/name.txt' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.12' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/ZINC001142702963.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp-working.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/fort.21' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/temp.ZmatMOPAC' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/outputhex.log' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed/1.mol2.original' removed directory: `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/1.failed' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963.ism' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/input.ism' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963/ZINC001142702963-numbered.ism' removed directory: `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/ZINC001142702963' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.in-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.19' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.o-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/failure-reason' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.20' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/1.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/output.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.o-hex' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.in-wat' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/outputwat.log' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/output.solv' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/name.txt' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.12' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/ZINC001142702963.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp-working.mol2' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/fort.21' removed `/scratch/xiaobo/194367/xbs-8058088.45/failed/ZINC001142702963/1.failed/temp.ZmatMOPAC' removed 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